Methods and Materials for Producing 7-Carbon Monomers

ABSTRACT

This document describes biochemical pathways for producing pimeloyl-CoA using a polypeptide having the enzymatic activity of a hydroperoxide lyase to form non-3-enal and 9-oxononanoate from 9-hydroxyperoxyoctadec-10,12-dienoate. Non-3-enal and 9-oxononanoate can be enzymatically converted to pimeloyl-CoA or a salt thereof using one or more polypeptides having the activity of a dehydrogenase, a CoA ligase, an isomerase, a reductase, a thioesterase, a monooxygenase, a hydratase, and/or a thiolase. Pimeloyl-CoA can be enzymatically converted to pimelic acid, 7-aminoheptanoic acid, 7-hydroxyheptanoic acid, heptamethylenediamine, or 1,7-heptanediol, or corresponding salts thereof. This document also describes recombinant microorganisms producing pimeloyl-CoA, as well as pimelic acid, 7-aminoheptanoic acid, 7-hydroxyheptanoic acid, heptamethylenediamine, and 1,7-heptanediol, or corresponding salts thereof.

CROSS-REFERENCE TO RELATED APPLICATIONS

The present application claims the benefit of U.S. Provisional Application Ser. No. 62/289,877, filed Feb. 1, 2016, which is incorporated herein by reference in its entirety.

SEQUENCE LISTING

The instant application contains a Sequence Listing which has been submitted electronically in ASCII format and is hereby incorporated by reference in its entirety. Said ASCII copy, created on Jan. 31, 2017, is named 12444_0626-00000_SL.txt and is 176,758 bytes in size.

TECHNICAL FIELD

This invention provides methods for biosynthesizing 7-carbon monomers. For example, the present invention provides methods for making two 9-carbon monomers from an 18-carbon intermediate and enzymatically converting the two 9-carbon monomers to 7-carbon monomers. For example, the present invention provides methods for making non-3-enal and 9-oxononanoate using a polypeptide having the activity of a hydroperoxide lyase and enzymatically converting non-3-enal and 9-oxononanoate to pimeloyl-CoA or a salt thereof using one or more polypeptides having the activity of a dehydrogenase, a CoA ligase, an isomerase, a reductase, a thioesterase, a monooxygenase, a hydratase, and/or a thiolase, or methods using microorganisms expressing one or more of such polypeptides. This invention also provides methods for converting pimeloyl-CoA or a salt thereof to one or more of pimelic acid, 7-aminoheptanoic acid, 7-hydroxyheptanoic acid, heptamethylenediamine, and 1,7-heptanediol, or corresponding salts thereof, using one or more polypeptides having the activity of a thioesterase, a CoA ligase, a CoA transferase, a dehydrogenase, a reductase, an acetyltransferase, a deacylase, and/or a transaminase or methods using recombinant microorganisms expressing one or more such polypeptides.

BACKGROUND

Nylons are synthetic polymers composed of polyamides, which are generally synthesized by the condensation polymerization of a diamine with a dicarboxylic acid. Similarly, nylons also may be produced by the condensation polymerization of lactams. Nylon 7 is produced by polymerisation of 7-aminoheptanoic acid, whereas Nylon 7,7 is produced by condensation polymerisation of pimelic acid and heptamethylenediamine. No economically cost competitive petrochemical routes exist to producing the monomers for Nylon 7 and Nylon 7,7.

Given the lack of economically cost competitive petrochemical monomer feedstocks, biotechnology offers an alternative approach via biocatalysis. Biocatalysis is the use of biological catalysts, such as enzymes, to perform biochemical transformations of, for example, bioderived feedstocks and petrochemical feedstocks, which can both be viable starting materials for the biocatalysis processes.

SUMMARY

Accordingly, against this background, it is clear that there is a need for sustainable methods for producing one or more of pimelic acid, 7-aminoheptanoate, 7-hydroxyheptanoate, heptamethylenediamine, and 1,7-heptanediol, or derivatives thereof, wherein the methods are biocatalyst based. This document is based at least in part on the discovery that it is possible to construct biochemical pathways using, inter alia, a polypeptide having the activity of a hydroperoxide lyase to produce two C9 (9-carbon) aliphatic molecules from a single C18 (18-carbon) molecule, and converting the two C9 molecules in one or more enzymatic steps to pimelic acid, 7-aminoheptanoic acid, 7-hydroxyheptanoic acid, heptamethylenediamine, or 1,7-heptanediol, or corresponding salts thereof. In particular, this document is based at least in part on the discovery that it is possible to construct biochemical pathways using, inter alia, a polypeptide having the activity of a hydroperoxide lyase to produce non-3-enal and 9-oxononanoate from 9-hydroxyperoxyoctadec-10,12-dienoate and converting at least one of non-3-enal and 9-oxononanoate in one or more enzymatic steps to pimelic acid, 7-aminoheptanoic acid, 7-hydroxyheptanoic acid, heptamethylenediamine or 1,7-heptanediol. Pimelic acid and pimelate, 7-hydroxyheptanoic acid and 7-hydroxyheptanoate, 9-oxononanoate and 9-oxononanoic acid, and 7-aminoheptanoic and 7-aminoheptanoate are used interchangeably herein to refer to the compounds in any of their neutral or ionized forms, including any salt forms thereof. It is understood by those skilled in the art that the specific form will depend on pH.

For compounds containing carboxylic acid groups such as organic monoacids, hydroxyacids, aminoacids, and dicarboxylic acids, these compounds may be formed or converted to their ionic salt form when an acidic proton present in the parent compound either is replaced by a metal ion, e.g., an alkali metal ion, an alkaline earth ion, or an aluminum ion; or coordinates with an organic base. Acceptable organic bases include ethanolamine, diethanolamine, triethanolamine, tromethamine, N-methylglucamine, and the like. Acceptable inorganic bases include aluminum hydroxide, calcium hydroxide, potassium hydroxide, sodium carbonate, sodium hydroxide, and the like. The salt can be isolated as is from the system as the salt or converted to the free acid by reducing the pH to below the pKa through addition of acid or treatment with an acidic ion exchange resin.

For compounds containing amine groups such as, but not limited to, organic amines, aminoacids, and diamines, these compounds may be formed or converted to their ionic salt form by addition of an acidic proton to the amine to form the ammonium salt, formed with inorganic acids such as hydrochloric acid, hydrobromic acid, sulfuric acid, nitric acid, phosphoric acid, and the like; or formed with organic acids such as acetic acid, propionic acid, hexanoic acid, cyclopentanepropionic acid, glycolic acid, pyruvic acid, lactic acid, malonic acid, succinic acid, malic acid, maleic acid, fumaric acid, tartaric acid, citric acid, benzoic acid, 3-(4-hydroxybenzoyl)benzoic acid, cinnamic acid, mandelic acid, methanesulfonic acid, ethanesulfonic acid, 1,2-ethanedisulfonic acid, 2-hydroxyethanesulfonic acid, benzenesulfonic acid, 2-naphthalenesulfonic acid, 4-methylbicyclo-[2.2.2]oct-2-ene-1-carboxylic acid, glucoheptonic acid, 4,4′-methylenebis-(3-hydroxy-2-ene-1-carboxylic acid), 3-phenylpropionic acid, trimethylacetic acid, tertiary butylacetic acid, lauryl sulfuric acid, gluconic acid, glutamic acid, hydroxynaphthoic acid, salicylic acid, stearic acid, muconic acid, and the like. Acceptable so inorganic bases are known in the art and include aluminum hydroxide, calcium hydroxide, potassium hydroxide, sodium carbonate, sodium hydroxide, and the like. The salt can be isolated as is from the system as a salt or converted to the free amine by raising the pH to above the pKb through addition of base or treatment with a basic ion exchange resin.

For compounds containing both amine groups and carboxylic acid groups such as, but not limited to aminoacids, these compounds may be formed or converted to their ionic salt form by either 1) acid addition salts, formed with inorganic acids such as hydrochloric acid, hydrobromic acid, sulfuric acid, nitric acid, phosphoric acid, and the like; or formed with organic acids such as acetic acid, propionic acid, hexanoic acid, cyclopentanepropionic acid, glycolic acid, pyruvic acid, lactic acid, malonic acid, succinic acid, malic acid, maleic acid, fumaric acid, tartaric acid, citric acid, benzoic acid, 3-(4-hydroxybenzoyl)benzoic acid, cinnamic acid, mandelic acid, methanesulfonic acid, ethanesulfonic acid, 1,2-ethanedisulfonic acid, 2-hydroxyethanesulfonic acid, benzenesulfonic acid, 2-naphthalenesulfonic acid, 4-methylbicyclo-[2.2.2]oct-2-ene-1-carboxylic acid, glucoheptonic acid, 4,4′-methylenebis-(3-hydroxy-2-ene-1-carboxylic acid), 3-phenylpropionic acid, trimethylacetic acid, tertiary butylacetic acid, lauryl sulfuric acid, gluconic acid, glutamic acid, hydroxynaphthoic acid, salicylic acid, stearic acid, muconic acid, and the like. Acceptable inorganic bases include aluminum hydroxide, calcium hydroxide, potassium hydroxide, sodium carbonate, sodium hydroxide, and the like; or 2) when an acidic proton present in the parent compound either is replaced by a metal ion, e.g., an alkali metal ion, an alkaline earth ion, or an aluminum ion; or coordinates with an organic base. Acceptable organic bases are known in the art and include ethanolamine, diethanolamine, triethanolamine, tromethamine, N-methylglucamine, and the like. Acceptable inorganic bases are known in the art and include aluminum hydroxide, calcium hydroxide, potassium hydroxide, sodium carbonate, sodium hydroxide, and the like. The salt can be isolated as is from the system or converted to the free acid by reducing the pH to below the pKa through addition of acid or treatment with an acidic ion exchange resin.

It has been discovered that appropriate non-natural pathways, feedstocks, microorganisms, attenuation strategies to the microorganism's biochemical network, and cultivation strategies may be combined to efficiently produce pimeloyl-CoA as a C7 (7-carbon) building block, or convert pimeloyl-CoA to other C7 building blocks such as pimelic acid, 7-aminoheptanoic acid, 7-hydroxyheptanoic acid, heptamethylenediamine, or 1,7-heptanediol.

In some embodiments, a terminal carboxyl group can be enzymatically formed using a polypeptide having the activity of a thioesterase, a CoA transferase, a CoA ligase, an aldehyde delhydrogenase, a succinate-semialdehyde dehydrogenase, a 5-oxopentanoate dehydrogenase, a 6-oxohexanoate dehydrogenase, or a 7-oxoheptanoate dehydrogenase. See FIG. 3.

In some embodiments, a terminal amine group can be enzymatically formed using a polypeptide having the activity of a w-transaminase or a deacylase. See FIG. 4 and FIG. 5. The polypeptide having the activity of a w-transaminase can have at least 70% sequence identity to any one of the amino acid sequences set forth in SEQ ID NOs: 7-12. Furthermore, the polypeptide having the activity of a ω-transaminase can have at least 70% sequence identity to any one of the amino acid sequences set forth in SEQ ID NOs: 7-12 and be capable of transferring at least one amine group separated from a carbonyl group by at least one methylene insertion.

In some embodiments, a terminal hydroxyl group can be enzymatically formed using a polypeptide having the activity of an alcohol dehydrogenase. See FIG. 4 and FIG. 7.

In one aspect, this document features a method of producing non-3-enal and 9-oxononanoate from 9-hydroxyperoxyoctadec-10,12-dienoate using a polypeptide having the activity of a hydroperoxide lyase classified under EC 4.2.99.-.

In any of the methods, non-3-enal and 9-oxononanoate can be enzymatically produced from 9-hydroxyperoxyoctadec-10,12-dienoate, which itself can be enzymatically produced from octadecanoyl-CoA using one or more polypeptides having the activity of a delta9-desaturase, a delta12-desaturase, a thioesterase, and/or a 9 lipoxygenase. The polypeptide having the activity of a delta9-desaturase can be classified under EC 1.14.19.1, such as, for example, the gene product of Le-FAD1 from Lentinula edodes (UniProtKB Accession No. Q76C19), the gene product of SCD1 from Mesocricetus auratus (UniProtKB Accession No. A7LCI9), an acyl-CoA-delta9-3a-desaturase from Dendrolimus punctatus (UniProtKB Accession No. B7SB75), the gene product of scd1 from Rattus norvegicus (UniProtKB Accession No. P07308), the gene product of PF3D7_0511200 from Plasmodium falciparum (UniProtKB Accession No. Q8I0W9), or the gene product of desB1 from Bombus lucorum (UniProtKB Accession No. A5CKE1).

The polypeptide having the activity of a delta12-desaturase can be classified under EC 1.14.19.6, such as, for example, the gene product of D12Des from Acheta domesticus (UniProtKB Accession No. B7SB9I), the gene product of FAD2 from Gossypium hirsutum (UniProtKB Accession No. Q8W2B9), the gene product of CFad6 from Chlorella vulgaris (UniProtKB Accession No. D3U658), a delta12 fatty acid desaturase from Triadica sebifera (UniProtKB Accession No. A5J295), the gene product of Pc-fad2 from Phanerochaete chrysosporium (UniProtKB Accession No. D4Q8H2), the gene product of Cs-fad2 from Ceriporiopsis subvermispora (UniProtKB Accession No. D4Q8S6), or the gene product of AN1037.2 from Emericella nidulans (UniProtKB Accession No. Q5BEJ3).

The polypeptide having the activity of a thioesterase can be classified under EC 3.1.2.-, such as, for example, the gene product of BT_2075 from Bacteroides thetaiotaomicron (strain ATCC 29148/DSM 2079/NCTC 10582/E50/VPI-5482) (GenBank Accession No. AAO77182.1, SEQ ID NO: 20), the gene product of lp_0708 from Lactobacillus plantarum (strain ATCC BAA-793/NCIMB 8826/WCFS1) (GenBank Accession No. CCC78182.1, SEQ ID NO: 22), the gene product of CPF_2954 from Clostridium perfringens (strain ATCC 13124/DSM 756/JCM 1290/NCIMB 6125/NCTC 8237/Type A) (GenBank Accession No. ABG82470.1, SEQ ID NO: 18), or the gene product of HMPREF0077_1317 from Anaerococcus tetradius ATCC 35098 (GenBank Accession No. EEI82564.1, SEQ ID NO: 23).

The polypeptide having the activity of a 9-lipoxygenase can be classified, for example, under EC 1.13.11.58, EC 1.13.11.60, EC 1.13.11.61, or EC 1.13.11.62, such as, for example, an allene oxide synthase-lipoxygenase protein from Plexaura homromalla (UniProtKB Accession No. O16025), a Psi-producing oxygenase A from Emericella nidulans (UniProtKB Accession No. Q6RET3), a 5,8-linoleate diol synthase from Aspergillus fumigatus (UniProtKB Accession No. C1KH66), or a linoleate dial synthase from Gaeumannomyces graminis (UniProtKB Accession No. Q9UUS2).

The method includes enzymatically converting non-3-enal to azelaic acid via two alternative enzymatic pathways. The method also includes enzymatically converting 9-oxononanoate to azelaic acid.

In one aspect, the method includes converting non-3-enal to azelaic acid using one or more polypeptides having the enzymatic activities of an aldehyde dehydrogenase, a CoA ligase, a dodeceoyl-CoA isomerase, a dodecenoyl-coA isomerase, a trans-2-enoyl-CoA reductase, a thioesterase, a monooxygenase, an alcohol dehydrogenase, a succinate semialdehyde dehydrogenase, a 5-oxopentanoate dehydrogenase, a 6-oxohexanoate dehydrogenase, and/or a 7-oxoheptanoate dehydrogenase.

The polypeptide having the activity of an aldehyde dehydrogenase can be classified under EC 1.2.1.-, for example, EC 1.2.1.3, EC 1.2.1.4, EC 1.2.1.5, or EC 1.2.1.48, such as, for example, the gene product of Bt-aldh from Geobacillus thermoleovorans B23 (UniProtKB Accession No. Q9FAB1), the gene product of dhaS from Bacillus subtilis (UniProtKB Accession No. O34660), the gene product of ALD5 from Saccharomyces cerevisiae (UniProtKB Accession No. A6ZR27), the gene product of ALDH2C4 from Arabidopsis thaliana (UniProtKB Accession No. Q56YU0), the gene product of aldh7 from Rhodococcus ruber (UniProtKB Accession No. Q840S9), the gene product of alkH from Pseudomonas oleovorans (UniProtKB Accession No. P12693), the gene product of ald1 from Acinetobacter sp. M-1 (UniProtKB Accession No. Q9FDS1), or the gene product of acoD from Ralstonia eutropha (UniProtKB Accession No. P46368).

The polypeptide having the activity of a CoA ligase can be classified under EC 6.2.1.-, such as, for example, the gene product of acs6 from Brassica napus (UniProtKB Accession No. Q9FNT6), the gene product of PCS60 from Saccharomyces cerevisiae (UniProtKB Accession No. P38137), the gene product of alkK from Pseudomonas oleovorans (UniProtKB Accession No. Q00594), the gene product of ACSM5 from Homo sapiens (UniProtKB Accession No. Q6NUN0), or the gene product of alkK from Aeropyrum pernix (UniProtKB Accession No. Q9YF45).

The polypeptide having the activity of a dodecenoyl-CoA isomerase can be classified under EC 5.3.3.8, such as, for example, the gene product of ECI1 from Saccharomyces cerevisiae (SEQ ID NO: 17 and SEQ ID NO: 19).

The polypeptide having the activity of a trans-2-enoyl-CoA reductase can be classified under EC 1.3.1.38, EC 1.3.1.44, or EC 1.3.1.8. The polypeptide having the activity of a thioesterase can be classified under EC 3.1.2.-. The polypeptide having the activity of a monooxygenase can be classified under EC 1.14.14.1, EC 1.14.14.3, EC 1.14.15.1, or EC 1.14.15.3. The polypeptide having the activity of an alcohol dehydrogenase can be classified under EC 1.1.1.-, such as, for example, a 4-hydroxybutanoate dehydrogenase classified under EC 1.1.1.61, such as, for example, the gene product of gabD from Escherichia coli (Bartsch et al., J. Bacteriol., 1990, 172(12), 7035), or a 6-hydroxyhexanoate dehydrogenase classified under EC 1.1.1.258, such as, for example, the gene product of chnD from Acinetobacter sp. NCIMB9871 (Donoghue et al., Eur. J. Biochem, 1975, 60: 1-7). The polypeptide having the activity of a succinate semialdehyde dehydrogenase can be classified under EC 1.2.1.16, EC 1.2.1.24, or EC 1.2.1.79. The polypeptide having the activity of a 5-oxopentanoate dehydrogenase can be classified under EC 1.2.1.20, such as that encoded by cpnE from Comamonas sp. The polypeptide having the activity of a 6-oxohexanoate dehydrogenase can be classified under EC 1.2.1.63, such as that encoded by chnE from Acinetobacter sp., and the polypeptide having the activity of a 7-oxoheptanoate dehydrogenase can be classified under EC 1.2.1.- (e.g., the gene product of thnG from Sphingomonas macrogolitabida).

In an alternative aspect, the method includes converting non-3-enal to azelaic acid as using one or more polypeptides having the enzymatic activities of an enal isomerase, an enoate reductase, an aldehyde dehydrogenase, a monooxygenase, an alcohol dehydrogenase, a succinate semialdehyde dehydrogenase, a 5-oxopentanoate dehydrogenase, a 6-oxohexanoate dehydrogenase, and/or a 7-oxoheptanoate dehydrogenase. The polypeptide having the activity of an enal isomerase can be classified under EC 5.3.3.-, such as, for example, the gene product of ECI1 from Saccharomyces cerevisiae (SEQ ID NO: 17 and SEQ ID NO: 19); Geisbrecht et al J. Biol. Chem, 1998 273 (50) 33184-33191.) The polypeptide having the activity of an enoate reductase can be classified under EC 1.3.1.31. The polypeptide having the activity of an aldehyde dehydrogenase can be classified under EC 1.2.1.-, for example, EC 1.2.1.3, EC 1.2.1.4, EC 1.2.1.5, or EC 1.2.1.48. The polypeptide having the activity of a monooxygenase can be classified under EC 1.14.14.1, EC 1.14.14.3, EC 1.14.15.1, or EC 1.14.15.3. The polypeptide having the activity of an alcohol dehydrogenase can be classified under EC 1.1.1.-, for example, a 4-hydroxybutanoate dehydrogenase classified under EC 1.1.1.61, such as, for example, the gene product of gabD from Escherichia coli (Bartsch et al., J. Bacteriol., 1990, 172(12), 7035), or a 6-hydroxy hexanoate dehydrogenase classified under EC 1.1.1.258, such as, for example, the gene product of chnD from Acinetobacter sp. NCIMB9871 (Donoghue et al., Eur. J. Biochem, 1975, 60:1-7).

The polypeptide having the activity of a succinate semialdehyde dehydrogenase can be classified under EC 1.2.1.16, EC 1.2.1.24, or EC 1.2.1.79, such as, for example, the gene product of ALDH5F1 from Arabidopsis thaliana (UniProtKB Accession No. Q9SAK4), the gene product of araE from Azospirilluim brasilense (UniProtKB Accession No. Q1JUP4), the gene product of Ssadh from Drosophila melanogaster (UniProtKB Accession No. Q9VBP6), the gene product of ALDH5A1 from Gorilla gorilla (UniProtKB Accession No. Q6A2H1), the gene product of ALDH5A1 from Hylobates lar (UniProtKB Accession No. Q3MSM3), the gene product of ssadh from Lucilia cuprina (UniProtKB Accession No. B0JFD4), the gene product of ALDH5A1 from Pan paniscus (UniProtKB Accession No. Q3MSM4), the gene product of ALDH5A1 from Pan troglodytes (UniProtKB Accession No. Q6A2H0), the gene product of ALDH5A1 from Pongo abelii (UniProtKB Accession No. Q6A2H2), the gene product of ALDH5A1 from Pongo pygmaeus (UniProtKB Accession No. Q6A2H2), or the gene product of gapN−1 from Sulfolobus solfataricus (UniProtKB Accession No. Q97XS9).

The polypeptide having the activity of a 5-oxopentanoate dehydrogenase can be classified under EC 1.2.1.20, such as that encoded by cpnE from Comamonas sp. The polypeptide having the activity of a 6-oxohexanoate dehydrogenase can be classified under EC 1.2.1.63, such as that encoded by chnE from Acinetobacter sp., and the polypeptide having the activity of a 7-oxoheptanoate dehydrogenase can be classified under EC 1.2.1.- (e.g., the gene product of thnG from Sphingomonas macrogolitabida).

In a further aspect, the method includes converting 9-oxononanoate to azelaic acid using a polypeptide classified under EC 1.2.1.-, such as EC 1.2.1.3, EC 1.2.1.16, EC 1.2.1.20, EC 1.2.1.24, EC 1.2.1.63, or EC 1.2.1.79. The polypeptides classified under EC 1.2.1.3 have the activity of an aldehyde dehydrogenase. The polypeptides classified under EC 1.2.1.16, EC 1.2.1.24, or EC 1.2.1.79 have the activity of a succinate semialdehyde dehydrogenase, such as, for example, the gene product of ALDH5F1 from Arabidopsis thaliana (UniProtKB Accession No. Q9SAK4), the gene product of araE from Azospirillum brasilense (UniProtKB Accession No. Q1JUP4), the gene product of Ssadh from Drosophila melanogaster (UniProtKB Accession No. Q9VBP6), the gene product of ALDH5A1 from Gorilla gorilla (UniProtKB Accession No. Q6A2H1), the gene product of ALDH5A from Hylobates lar (UniProtKB Accession No. Q3MSM3), the gene product of ssadh from Lucilia cuprina (UniProtKB Accession No. B0JFD4), the gene product of ALDH5A1 from Pan paniscus (UniProtKB Accession No. Q3MSM4), the gene product of ALDH5A1 from Pan troglodytes (UniProtKB Accession No. Q6A2H0), the gene product of ALDH5A from Pongo abelii (UniProtKB Accession No. Q6A2H2), the gene product of ALDH5A1 from Pongo pygmaeus (UniProtKB Accession No. Q6A2H2), or the gene product of gapN−1 from Sulfolobus solfataricus (UniProtKB Accession No. Q97XS9). The polypeptides classified under EC 1.2.1.20 have the activity of a 5-oxopentanoate dehydrogenase, such as that encoded by cpnE from Comamonas sp. The polypeptides classified under EC 1.2.1.63 have the activity of a 6-oxohexanoate dehydrogenase, such as that encoded by chnE from Acinetobacter sp. Further polypeptides classified under EC 1.2.1.- have the activity of a 7-oxoheptanoate dehydrogenase (e.g., the gene product of thnG from Sphingomonas macrogolitabida).

In the above-described enzymatic pathways, both non-3-enal and 9-oxononanoate are converted to azelaic acid. Azelaic acid is then converted to pimeloyl-CoA using one or more polypeptides having the enzymatic activities of a CoA ligase, an acyl-CoA dehydrogenase, an enoyl-CoA hydratase, a 3-hydroxyacyl-CoA dehydrogenase, a 3-oxoacyl-ACP reductase, and/or β-ketothiolase.

The polypeptide having the activity of a CoA ligase can be classified under EC 6.2.1.-, such as, for example, the gene product of acs6 from Brassica napus (UniProtKB Accession No. Q9FNT6), the gene product of PCS60 from Saccharomyces cerevisiae (UniProtKB Accession No. P38137), the gene product of alkK from Pseudomonas oleovorans (UniProtKB Accession No. Q00594), the gene product of ACSM5 from Homo sapiens (UniProtKB Accession No. Q6NUN0), or the gene product of alkK from Aeropyrum pernix (UniProtKB Accession No. Q9YF45). The polypeptide having the activity of an acyl-CoA dehydrogenase can be classified under EC 1.3.8.-, such as EC 1.3.8.6, EC 1.3.8.7, or EC 1.3.8.8. The polypeptide having the activity of an enoyl-CoA hydratase can be classified under EC 4.2.1.17 or EC 4.2.1.119. The polypeptide having the activity of a 3-hydroxyacyl-CoA dehydrogenase can be classified under EC 1.1.1.35, EC 1.1.1.36, or EC 1.1.1.157, and the polypeptide having the activity of a 3-oxoacyl-ACP reductase may be classified, for example, under EC 1.1.1.100. The polypeptide having the activity of β-ketothiolase can be classified under EC 2.3.1.16 or EC 2.3.1.174. The polypeptide having the activity of a β-ketothiolase is capable of converting 3-oxo-azelaoyl-CoA to pimeloyl-CoA.

Any of the methods further can include enzymatically converting pimeloyl-CoA to pimelic acid, 7-aminoheptanoate, 7-hydroxyheptanoate, heptamethylenediamine, or 1,7-heptanediol or their corresponding salts in one or more steps.

For example, pimeloyl-CoA can be enzymatically converted to pimelic acid using one or more polypeptides having the activity of a thioesterase, a CoA ligase, a CoA transferase, an aldehyde dehydrogenase, a 5-oxopentanoate dehydrogenase, a 6-oxohexanoate dehydrogenase, a 7-oxoheptanoate dehydrogenase, and/or a succinate-semialdehyde dehydrogenase. See FIG. 3.

For example, pimeloyl-CoA can be enzymatically converted to 7-aminoheptanoate using one or more polypeptides having the activity of an acetylating aldehyde dehydrogenase and/or a ω-transaminase. See FIG. 4.

For example, pimeloyl-CoA can be enzymatically converted to pimelate (pimelic acid) as previously described in FIG. 3, and pimelate can be enzymatically converted to 7-aminoheptanoate using one or more polypeptides having the enzymatic activity of a carboxylate reductase and/or a ω-transaminase. See FIG. 4. The polypeptide having the activity of a ω-transaminase can have at least 70% sequence identity to any one of the amino acid sequences set forth in SEQ ID NOs: 7-12.

For example, pimeloyl-CoA can be enzymatically converted to 7-hydroxyheptanoate using one or more polypeptides having the enzymatic activity of an acetylating aldehyde dehydrogenase and/or an alcohol dehydrogenase. In particular, pimeloyl-CoA can be enzymatically converted to 7-hydroxyheptanoate using one or more polypeptides having the enzymatic activity of an acetylating aldehyde dehydrogenase and one or more polypeptides having the enzymatic activity of a 4-hydroxybutanoate dehydrogenase, a 5-hydroxypentanoate dehydrogenase, and/or a 6-hydroxyhexanoate dehydrogenase. See FIG. 6.

For example, pimeloyl-CoA can be enzymatically converted to pimelate (pimelic acid) as previously described in FIG. 3, and pimelate can be enzymatically converted to 7-hydroxyheptanoate using one or more polypeptides having the enzymatic activity of a carboxylate reductase and/or an alcohol dehydrogenase. In particular, pimelate can be enzymatically converted to 7-hydroxyheptanoate using one or more polypeptides having the enzymatic activity of a carboxylate reductase and one or more polypeptides having the enzymatic activity of a 4-hydroxybutanoate dehydrogenase, a 5-hydroxypentanoate dehydrogenase, and/or a 6-hydroxyhexanoate dehydrogenase. See FIG. 6.

For example, 7-aminoheptanoate and 7-hydroxyheptanoate can be converted to heptamethylenediamine using one or more polypeptides having the activity of a carboxylate reductase, a ω-transaminase, an alcohol dehydrogenase, an N-acetyltransferase, and/or a deacylase. See FIG. 5.

The polypeptide having the activity of a carboxylate reductase can have at least 70% sequence identity to any one of the amino acid sequences set forth in SEQ ID NOs: 1-6. The polypeptide having the activity of a ω-transaminase can have at least 70% sequence identity to any one of the amino acid sequences set forth in SEQ ID NOs: 7-12. For example, pimeloyl-CoA can be converted to pimelate semialdehyde (see FIG. 3, FIG. 4, and FIG. 6), and subsequently pimelate semialdehyde can be converted to heptamethylenediamine using one or more polypeptides having the activity of a carboxylate reductase and/or a ω-transaminase. See FIG. 5.

S The polypeptide having the activity of a carboxylate reductase can have at least 70% sequence identity to any one of the amino acid sequences set forth in SEQ ID NO: 1-6. The polypeptide having the activity of a co-transaminase can have at least 70% sequence identity to any one of the amino acid sequences set forth in SEQ ID NOs: 7-12.

For example, pimeloyl-CoA can be converted to 7-hydroxyheptanoate (see FIG. 6), and subsequently 7-hydroxyheptanoate can be converted to 1,7-heptanediol using polypeptides having the activity of a carboxylate reductase and an alcohol dehydrogenase. See FIG. 7.

The polypeptide having the activity of a carboxylate reductase can have at least 70% sequence identity to any one of the amino acid sequences set forth in SEQ ID NOs: 1-6.

In any of the methods described herein, pimelic acid can be produced by forming the second terminal functional group in pimeloyl-CoA using a polypeptide having the activity of: (i) a thioesterase classified under EC 3.1.2.-, (ii) a CoA ligase classified under EC 6.2.1.-, such as EC 6.2.1.5 or EC 6.2.1.15, and/or (iii) a CoA transferase classified under EC 2.8.3.-, such as EC 2.8.3.8 or EC 2.8.3.12.

In any of the methods described herein, pimelic acid can be produced by forming the second terminal functional group in pimelate semialdehyde (also known as 7-oxoheptanoate) using a polypeptide having the activity of (i) an aldehyde dehydrogenase classified under EC 1.2.1.3, or (ii) a succinate semialdehyde dehydrogenase classified under EC 1.2.1.16, EC 1.2.1.24, or EC 1.2.1.79, a 5-oxopentanoate dehydrogenase classified under EC 1.2.1.-, for example, EC 1.2.1.20, such as that encoded by cpnE from Comamonas sp., a 6-oxohexanoate dehydrogenase classified under EC 1.2.1.63, such as that encoded by chnE from Acinetobacter sp., or a 7-oxoheptanoate dehydrogenase classified under EC 1.2.1.- (e.g., the gene product of thnG from Sphingomonas macrogolitabida). See FIG. 3.

In any of the methods described herein, 7-aminoheptanoic acid can be produced by forming the second terminal functional group in pimelate semialdehyde using a polypeptide having the activity of a ω-transaminase classified under EC 2.6.1.-. See FIG. 4.

In any of the methods described herein, 7-hydroxyheptanoic acid can be produced by forming the second terminal functional group in pimelate semialdehyde using a polypeptide having the activity of an alcohol dehydrogenase classified under EC 1.1.1.-, a 6-hydroxyhexanoate dehydrogenase classified under EC 1.1.1.258, such as, for example, the gene product of chnD from Acinetobacter sp. NCIMB9871 (Donoghue et al., Eur. J. Biochem, 1975, 60: 1-7); a 5-hydroxypentanoate dehydrogenase classified under EC 1.1.1.-, such as, for example, the gene product of cpnD from Comamonas sp. (Iwaki et al., Appl. Environ. Microbiol., 1999, 65(1):5158-5162), or a 4-hydroxybutanoate dehydrogenase classified under EC 1.1.1.61, such as, for example, the gene product of gabD from Escherichia coli (Bartsch et al., J. Bacteriol., 1990, 172(12), 7035). See FIG. 6.

In any of the methods described herein, heptamethylenediamine can be produced by forming a second terminal functional group in (i) 7-aminoheptanal using a polypeptide having the activity of a ω-transaminase classified under EC 2.6.1.-, such as, for example, EC 2.6.1.18, EC 2.6.1.19, EC 2.6.1.29, EC 2.6.1.48, or EC 2.6.1.82 or in (ii) N7-acetyl-1,7-diaminoheptane using a deacylase classified, for example, under EC 3.5.1.-, such as, for example, EC 3.5.1.62 or EC 3.5.1.82, such as that encoded by dag from Alcaligenes xylosoxydans xylosoxydans (Achromobacter xylosoxidans) (UniProtKB Accession No. P94211). See FIG. 5.

In any of the methods described herein, 1,7-heptanediol can be produced by forming the second terminal functional group in 7-hydroxyheptanal using a polypeptide having the activity of an alcohol dehydrogenase classified under EC 1.1.1.- (e.g., EC 1.1.1.1, EC 1.1.12, EC 1.1.1.21, or EC 1.1.1.184), such as that encoded by YMR318C from Saccharomyces cerevisiae, yqhD from Escherichia coli, or as represented by GenBank Accession No. CAA81612.1 (SEQ ID NO: 21). See FIG. 7.

In some embodiments, the biological feedstock can be or can derive from, monosaccharides, disaccharides, lignocellulose, hemicellulose, cellulose, lignin, levulinic acid and formic acid, triglycerides, glycerol, fatty acids, agricultural waste, condensed distillers' solubles, plant oils, or municipal waste.

In some embodiments, the non-biological feedstock can be or can derive from natural gas, syngas, CO₂/H₂, methanol, ethanol, benzoate, non-volatile residue (NVR) or a caustic wash waste stream from cycloheptane oxidation processes, or terephthalic acid/isophthalic acid mixture waste streams.

In some embodiments, the microorganism's tolerance to high concentrations of one or more C7 (7-carbon) building blocks is improved through continuous cultivation in a selective environment.

In some embodiments, the microorganism's biochemical network is attenuated or augmented to (1) ensure the intracellular availability of acetyl-CoA or malonyl-CoA, (2) create an NADH or NADPH imbalance that may only be balanced via the formation of one or more C7 building blocks, (3) prevent degradation of central metabolites, central precursors leading to and including C7 building blocks, and/or (4) ensure efficient efflux from the cell.

As used herein, “attenuation” refers to downregulation or inactivation of gene expression.

In some embodiments, a cultivation strategy is used to achieve anaerobic, micro-aerobic, or aerobic cultivation conditions.

In some embodiments, the cultivation strategy includes limiting nutrients, such as limiting nitrogen, phosphate, or oxygen.

In some embodiments, one or more C7 building blocks are produced by a single type of microorganism, e.g., a recombinant microorganism containing one or more exogenous nucleic acids, using, for example, a fermentation strategy. In some embodiments, one or more C7 building blocks are produced by a single type of microorganism having one or more exogenous nucleic acids which encode polypeptides having the activity of a hydroxperoxide lyase, aldehyde dehydrogenase, a CoA ligase, a dodecenoyl-CoA isomerase, a trans-2-enoyl-CoA reductase, a thioesterase, a monooxygenase, an alcohol dehydrogenase, a succinate-semialdehyde dehydrogenase, a 5-oxopentanoate dehydrogenase, a 6-oxohexanoate dehydrogenase, a 7-oxoheptanoate dehydrogenase, an acyl-CoA dehydrogenase, an enoyl-CoA hydratase, a 3-hydroxyacyl-CoA dehydrogenase, a 3-oxoacyl CoA dehydrogenase, and/or a β-ketothiolase. Said microorganism produces pimeloyl-CoA from 9-hydroxyperoxyoctadec-10,12-dienoate. See FIG. 1.

In another aspect, this document features a recombinant microorganism that in includes at least one exogenous nucleic acid encoding a polypeptide having the activity of a hydroxperoxide lyase, an enal isomerase, an enoate reductase, an aldehyde dehydrogenase, a monooxygenase, an alcohol dehydrogenase, a succinate-semialdehyde dehydrogenase, a 5-oxopentanoate dehydrogenase, a 6-oxohexanoate dehydrogenase, a 7-oxoheptanoate dehydrogenase, a CoA ligase, an acyl-CoA dehydrogenase, an enoyl-CoA hydratase, a 3-hydroxyacyl-CoA dehydrogenase, a 3-oxoacyl CoA dehydrogenase, and/or a β-ketothiolase. Said microorganism produces pimeloyl-CoA from 9 hydroxyperoxyoctadec-10,12-dienoate. See FIG. 2.

In another aspect, this document features a recombinant microorganism that includes at least one exogenous nucleic acid encoding a polypeptide having the activity of an aldehyde dehydrogenase, a succinate-semialdehyde dehydrogenase, a 5-oxopentanoate dehydrogenase, a 6-oxohexanoate dehydrogenase, a 7-oxoheptanoate dehydrogenase, a CoA ligase, an acyl-CoA dehydrogenase, an enoyl-CoA hydratase, a 3-hydroxyacyl-CoA dehydrogenase, a 3-oxoacyl CoA dehydrogenase, and a β-ketothiolase. Said microorganism produces pimeloyl-CoA from 9-oxononanoate. See FIG. 1 and FIG. 2.

A microorganism producing pimeloyl-CoA further can include one or more polypeptides having the activity of: (i) a thioesterase, (ii) a CoA ligase, (iii) a CoA transferase, and/or (iv) an acetylating aldehyde dehydrogenase and one of a succinate-semialdehyde dehydrogenase, a 5-oxopentanoate dehydrogenase, a 6-oxohexanoate dehydrogenase, and/or a 7-oxoheptanoate dehydrogenase; the microorganism further producing pimelic acid or a salt thereof. See FIG. 3.

A microorganism producing pimeloyl-CoA further can include one or more polypeptides having the activity of an acetylating aldehyde dehydrogenase and/or a ω-transaminase, the microorganism further producing 7-aminoheptanoate or a salt thereof. A microorganism producing pimeloyl-CoA further can include one or more of the exogenous polypeptides as described directly above for producing pimelate, and a microorganism producing pimelate further can include one or more exogenous polypeptides having the activity of: carboxylate reductase and/or a ω-transaminase, the microorganism further producing 7-aminoheptanoate or a salt thereof. See FIG. 4.

A microorganism producing pimeloyl-CoA further can include one or more of the following exogenous polypeptides having the activity of: an acetylating aldehyde dehydrogenase, an alcohol dehydrogenase, a 4-hydroxybutanoate dehydrogenase, a 5$ hydroxypentanoate dehydrogenase, and a 6-hydroxyhexanoate dehydrogenase, the microorganism further producing 7-hydroxyheptanoate or a salt thereof. A microorganism producing pimeloyl-CoA further can include one or more of the exogenous polypeptides as described directly above for producing pimelate, and a microorganism producing pimelate further can include one or more polypeptides having the activity of carboxylate reductase and/or a ω-transaminase, the microorganism further producing 7-aminoheptanoate or a salt thereof. A microorganism producing pimeloyl-CoA further can include one or more exogenous polypeptides having the activity of: an acetylating aldehyde dehydrogenase, an alcohol dehydrogenase, a 4-hydroxybutanoate dehydrogenase, a 5-hydroxypentanoate dehydrogenase, and/or a 6-hydroxyhexanoate dehydrogenase, the microorganism further producing 7-hydroxyheptanoate or a salt thereof. A microorganism producing pimeloyl-CoA further can include one or more of the exogenous polypeptides as described directly above for producing pimelate, and a microorganism producing pimelate further can include one or more exogenous polypeptides having the activity of: a carboxylate reductase and an alcohol dehydrogenase, a 4-hydroxybutanoate dehydrogenase, a 5-hydroxypentanoate dehydrogenase, and/or a 6-hydroxyhexanoate dehydrogenase, the microorganism further producing 7-hydroxyheptanoate or a salt thereof. See FIG. 6.

A microorganism producing pimeloyl-CoA further can include one or more of the exogenous polypeptides as described above for producing 7-aminoheptanoate or 7-hydroxyheptanoate, and a microorganism producing 7-aminoheptanoate or 7-hydroxyheptanoate can further include one or more of the exogenous polypeptides having the activity of: a carboxylate reductase, ω-transaminase, an alcohol dehydrogenase, an N-acetyltransferase, and/or a deacylase, said microorganism further producing heptamethylenediamine. A microorganism producing pimelate semialdehyde (see FIG. 3, FIG. 4, and FIG. 6) can further include one or more polypeptides having the activity of a carboxylate reductase and/or a ω-transaminase, said microorganism further producing heptamethylenediamine or a salt thereof. See FIG. 5.

A microorganism producing pimeloyl-CoA further can include one or more of the exogenous polypeptides as described above for producing 7-hydroxyheptanoate, and a microorganism producing 7-hydroxyheptanoate can further include one or more of the exogenous polypeptides having the activity of a carboxylate reductase and/or an alcohol dehydrogenase, the microorganism further producing 1,7-heptanediol. See FIG. 7.

Any of the recombinant microorganisms described herein further can include one or more of exogenous polypeptides having the activity of: a delta9-desaturase, a delta12-desaturase, a thioesterase, and/or a 9-lipoxygenase.

Any of the recombinant microorganisms can be a prokaryote, such as a prokaryote from a genus selected from Escherichia, Clostridia, Corynebacteria, Cupriavidus, Pseudomonas, Delftia, Bacillus, Lactobacillus, Lactococcus, and Rhodococcus. For example, the prokaryote can be selected from Escherichia coli, Clostridium ljungdahlii, Clostridium autoethanogenum, Clostridium kluyveri, Corynebacterium glutamicum, Cupriavidus necator, Cupriavidus metallidurans. Pseudomonas fluorescens, Pseudomonas putida, Pseudomonas oleavorans, Delftia acidovorans, Bacillus subtillis, Lactobacillus delbrueckii, Lactococcus lactis, and Rhodococcus equi. Such prokaryotes also can be sources of genes for constructing recombinant cells described herein that are capable of producing C7 building blocks.

Any of the recombinant microorganisms can be a eukaryote such as a eukaryote from a genus selected from Aspergillus, Saccharomyces, Pichia, Yarrowia, Issatchenkia, Debaryomyces, Arxula, and Kluyveromyces. For example, the eukaryote can be selected from Aspergillus niger, Saccharomyces cerevisiae, Pichia pastoris, Yarrowia lipolytica, Issathenkia orientalis, Debaryomyces hansenii, Arxula adenoinivorans, and Kluyveromyces lactis. Such eukaryotes also can be sources of genes for constructing recombinant cells described herein that are capable of producing C7 building blocks.

Any of the recombinant microorganisms described herein further can include attenuation of one or more of the following enzymes: a polyhydroxyalkanoate synthase, an acetyl-CoA thioesterase, a phosphotransacetylase forming acetate, an acetate kinase, a lactate dehydrogenase, a menaquinol-fumarate oxidoreductase, an alcohol dehydrogenase forming ethanol, a triose phosphate isomerase, a pyruvate decarboxylase, a glucose-6-phosphate isomerase, an NADH-consuming transhydrogenase, an NADH-specific glutamate dehydrogenase, an NADH/NADPH-utilizing glutamate dehydrogenase, a pimeloyl-CoA dehydrogenase, an acyl-CoA dehydrogenase accepting C7 building blocks and central precursors as substrates, a butyryl-CoA dehydrogenase, or an adipyl-CoA synthetase.

Any of the recombinant microorganisms described herein further can overexpress one or more genes encoding: an acetyl-CoA synthetase, a 6-phosphogluconate dehydrogenase; a transketolase; a puridine nucleotide transhydrogenase; a glyceraldehyde-3P-delhydrogenase; a malic enzyme; a glucose-6-phosphate dehydrogenase; a glucose dehydrogenase; a fructose 1,6 diphosphatase; a L-alanine dehydrogenase; a L-glutamate dehydrogenase; a formate dehydrogenase; a L-glutamine synthetase; a diamine transporter; a dicarboxylate transporter; and/or a multidrug transporter.

In another aspect, this document features a non-naturally occurring microorganism comprising at least one exogenous nucleic acid encoding at least one polypeptide having the activity of at least one enzyme, at least one substrate, and at least one product, as depicted in any one of FIG. 1 to 7.

In another aspect, this document features a nucleic acid construct or expression vector comprising a polynucleotide encoding a polypeptide having carboxylate reductase activity, wherein the polynucleotide is operably linked to one or more heterologous control sequences that direct production of the polypeptide and wherein the polypeptide having carboxylate reductase activity is selected from: (a) a polypeptide having at least 70% sequence identity to the polypeptide of SEQ ID NO: 1; (b) a polypeptide having at least 70% sequence identity to the polypeptide of SEQ ID NO: 2; (c) a polypeptide having at least 70% sequence identity to the polypeptide of SEQ ID NO: 3; (d) a polypeptide having at least 70% sequence identity to the polypeptide of SEQ ID NO: 4, (e) a polypeptide having at least 70% sequence identity to the polypeptide of SEQ ID NO: 5 and (f) a polypeptide having at least 70% sequence identity to the polypeptide of SEQ ID NO: 6.

In another aspect, this document features a nucleic acid construct or expression vector comprising a polynucleotide encoding a polypeptide having ω-transaminase activity, wherein the polynucleotide is operably linked to one or more heterologous control sequences that direct production of the polypeptide and wherein the polypeptide having ω-transaminase activity is selected from: (a) a polypeptide having at least 70% sequence identity to the polypeptide of SEQ ID NO: 7; (b) a polypeptide having at least 70% sequence identity to the polypeptide of SEQ ID NO: 8; (c) a polypeptide having at least 70% sequence identity to the polypeptide of SEQ ID NO: 9; (d) a polypeptide having at least 70% sequence identity to the polypeptide of SEQ ID NO: 10; (e) a polypeptide having at least 70% sequence identity to the polypeptide of SEQ ID NO: 11 or SEQ ID NO: 48; and (f) a polypeptide having at least 70% sequence identity to the polypeptide of SEQ ID NO: 12.

In another aspect, this document features a nucleic acid construct or expression vector comprising a polynucleotide encoding a polypeptide having hydroperoxide lyase activity, wherein the polynucleotide is operably linked to one or more heterologous control sequences that direct production of the polypeptide and wherein the polypeptide having hydroperoxide lyase activity is selected from: (a) a polypeptide having at least 70% sequence identity to the polypeptide of SEQ ID NO: 13 and (b) a polypeptide having at least 70% sequence identity to the polypeptide of SEQ ID NO: 14.

In another aspect, this document features a nucleic acid construct or expression vector comprising a polynucleotide encoding a polypeptide having enoate reductase activity, wherein the polynucleotide is operably linked to one or more heterologous control sequences that direct production of the polypeptide and wherein the polypeptide having enoate reductase activity is selected from: (a) a polypeptide having at least 70% sequence identity to the polypeptide of SEQ ID NO: 15 and (b) a polypeptide having at least 70% sequence identity to the polypeptide of SEQ ID NO: 16.

In another aspect, this document features a nucleic acid construct or expression vector comprising a polynucleotide encoding a polypeptide having isomerase activity, wherein the polynucleotide is operably linked to one or more heterologous control sequences that direct production of the polypeptide and wherein the polypeptide having isomerase activity is a polypeptide having at least 70% sequence identity to the polypeptide of SEQ ID NO: 17.

In another aspect, this document features a nucleic acid construct or expression vector comprising a polynucleotide encoding a polypeptide having thioesterase activity, wherein the polynucleotide is operably linked to one or more heterologous control sequences that direct production of the polypeptide and wherein the polypeptide having thioesterase activity is selected from: (a) a polypeptide having at least 70% sequence identity to the polypeptide of SEQ ID NO: 18, (b) a polypeptide having at least 70% sequence identity to the polypeptide of SEQ ID NO: 20, (c) a polypeptide having at least 70% sequence identity to the polypeptide of SEQ ID NO: 22, and (d) a polypeptide having at least 70% sequence identity to the polypeptide of SEQ ID NO: 23.

In another aspect, this document features a nucleic acid construct or expression vector comprising a polynucleotide encoding a polypeptide having alcohol dehydrogenase activity, wherein the polynucleotide is operably linked to one or more heterologous control sequences that direct production of the polypeptide and wherein the polypeptide having alcohol dehydrogenase activity is a polypeptide having at least 70% so sequence identity to the polypeptide of SEQ ID NO: 21.

In another aspect, this document features a composition comprising the nucleic acid construct or expression vector of embodiment 103 or 104.

In another aspect, this document features a culture medium comprising the nucleic acid construct or expression vector of embodiment 103 or 104.

In another aspect, this document features a non-naturally occurring biochemical network comprising 9-hydroxyperoxyoctadec-10,12-dienoate, an exogenous nucleic acid encoding a polypeptide having the activity of a hydroperoxide lyase classified under EC 4.2.99.-, and non-3-enal and 9-oxononanoate.

In another aspect, this document features a non-naturally occurring biochemical network comprising non-3-enoyl-CoA, an exogenous nucleic acid encoding a polypeptide having the activity of a dodecenoyl-CoA isomerase classified under EC 5.3.3.8, and non-2-enoyl-CoA.

In another aspect, this document features a non-naturally occurring biochemical network comprising non-2-enal, an exogenous nucleic acid encoding a polypeptide having the activity of an enoate reductase classified under EC 1.3.1.31, and nonanal.

In another aspect, this document features a non-naturally occurring biochemical network comprising nonanoic acid, an exogenous nucleic acid encoding a polypeptide having the activity of a monooxygenase classified under EC 1.14.14.- or EC 1.14.15.-, and a 9-hydroxynonanoic acid.

In another aspect, this document features means for producing pimeloyl-CoA, comprising culturing a non-naturally occurring microorganism comprising at least one exogenous nucleic acid encoding a polypeptide having the enzymatic activity of (i) a hydroperoxide lyase. (ii) an acetylating aldehyde dehydrogenase, (iii) a CoA ligase, (iv) a dodecenoyl-CoA isomerase or an enoate reductase, (v) a trans-2-enoyl-CoA reductase, as (vi) a thioesterase, (vii) a monooxygenase, (viii) an alcohol dehydrogenase, (ix) an aldehyde dehydrogenase classified under any of EC 1.2.1.3, EC 1.2.1.16, EC 1.2.1.20, EC 1.2.1.24, EC 1.2.1.63, or EC 1.2.1.79, (x) an acyl-CoA dehydrogenase, (xi) an enoyl-CoA hydratase, (xii) a 3-hydroxyacyl-CoA dehydrogenase or a 3-oxoacyl ACP reductase, and/or (xiii) a β-ketothiolase, expressed in a sufficient amount in said microorganism to produce pimeloyl-CoA.

In another aspect, this document features a bio-derived, bio-based or fermentation-derived product, wherein said product comprises: (i) a composition comprising at least one bio-derived, bio-based, or fermentation-derived compound according to embodiment 112; (ii) a bio-derived, bio-based, or fermentation-derived polymer comprising the bio-derived, bio-based, or fermentation-derived composition or compound of (i), or any combination thereof; (iii) a bio-derived, bio-based, or fermentation-derived resin comprising the bio-derived, bio-based, or fermentation-derived compound or bio-derived, bio-based, or fermentation-derived composition of (i) or any combination thereof or the bio-derived, bio-based, or fermentation-derived polymer of (ii) or any combination thereof; (iv) a molded substance obtained by molding the bio-derived, bio-based, or fermentation-derived polymer of (ii) or the bio-derived, bio-based, or fermentation-derived resin of (iii), or any combination thereof; (v) a bio-derived, bio-based, or fermentation-derived formulation comprising the bio-derived, bio-based, or fermentation-derived composition of (i), bio-derived, bio-based, or fermentation-derived compound of (i), bio-derived, bio-based, or fermentation-derived polymer of (ii), bio-derived, bio-based, or fermentation-derived resin of (iii), or bio-derived, bio-based, or fermentation-derived molded substance of (iv), or any combination thereof; and (vi) a bio-derived, bio-based, or fermentation-derived semi-solid or a non-semi-solid stream, comprising the bio-derived, bio-based, or fermentation-derived composition of (i), bio-derived, bio-based, or fermentation-derived compound of (i), bio-derived, bio-based, or fermentation-derived polymer of (ii), bio-derived, bio-based, or fermentation-derived resin of (iii), bio-derived, bio-based, or fermentation-derived formulation of (v), or bio-derived, bio-based, or fermentation-derived molded substance of (iv), or any combination thereof.

Embodiments 1-112 recite non-limiting example embodiments of the disclosure.

-   -   1. A method of producing non-3-enal and 9-oxononanoate in a         recombinant microorganism, said method comprising enzymatically         converting 9-hydroxyperoxyoctadec-10,12-dienoate to non-3-enal         and 9-oxononanoate using an exogenous polypeptide having the         activity of a hydroperoxide lyase classified under EC 4.2.99.-.     -   2. The method of embodiment 1, wherein said exogenous         polypeptide is the gene product of Cucumis sativus (GenBank         Accession No. AAF64041.1, SEQ ID NO: 13) or a polypeptide having         at least 70%, at least 80%, or at least 85% sequence identity         with the same or the gene product of Oryza sativa (GenBank         Accession No. BAG97978.1, SEQ ID NO: 14) or a polypeptide having         at least 70%, at least 80%, or at least 85% sequence identity         with the same.     -   3. The method of embodiment 1, further comprising enzymatically         converting non-3-enal to azelaic acid using a one or more         polypeptides, comprising at least one polypeptide having the         activity of a dodecenoyl-CoA isomerase classified under EC         5.3.3.8.     -   4. The method of embodiment 3, wherein said at least one         polypeptide having the activity of a dodecenoyl-CoA isomerase         classified under EC 5.3.3.8 enzymatically converts         non-3-enoyl-CoA to non-2-enoyl-CoA.     -   5. The method of embodiment 1, further comprising enzymatically         converting non-3-enal to azelaic acid using a one or more         polypeptides, comprising at least one polypeptide having the         activity of an enoate reductase classified under EC 1.3.1.31.     -   6. The method of embodiment 5, wherein said at least one         polypeptide having the activity of an enoate reductase         classified under EC 1.3.1.31 enzymatically is an enzymatic step         in converting non-3-enal to nonanal.     -   7. The method of embodiment 3 or embodiment 5, wherein said one         or more polypeptides comprises a polypeptide having the activity         of a monooxygenase classified under EC 1.14.14.- or EC         1.14.15.-, such as EC 1.14.14.1, EC 1.14.14.3, EC 1.14.15.1, or         EC 1.14.15.3.     -   8. The method of embodiment 7, wherein said polypeptide having         the activity of a monooxygenase converts nonanoic acid to         9-hydroxynonanoic acid.     -   9. A method of producing azelaic acid in a recombinant         microorganism, said method comprising the steps of enzymatically         converting 9-hydroxyperoxyoctadec-10,12-dienoate to non-3-enal         and 9-oxononanoate using an exogenous polypeptide having the         activity of a hydroperoxide lyase classified under EC 4.2.99.-         and enzymatically converting non-3-enal to azelaic acid using         one or more polypeptides, including at least one polypeptide         having the activity of a dodecenoyl-CoA isomerase classified         under EC 5.3.3.8 or at least one polypeptide having the activity         of an enoate reductase classified under EC 1.3.1.31.     -   10. The method of embodiment 9, wherein said one or more         polypeptides further comprises a polypeptide having the activity         of a monooxygenase classified under EC 1.14.14.- or EC         1.14.15.-, wherein said monooxygenase enzymatically converts         nonanoic acid to 9-hydroxynonanoic acid.     -   11. The method of embodiment 9, wherein said non-3-enal is         converted to azelaic acid using one or more polypeptides having         the enzymatic activities of an enal isomerase, an aldehyde         dehydrogenase, a CoA ligase, a dodecenoyl-CoA isomerase, a         trans-2-enoyl-CoA reductase, a thioesterase, a monooxygenase,         and/or an alcohol dehydrogenase.     -   12. The method of embodiment 11, wherein said aldehyde         dehydrogenase is classified under EC 1.2.1.3, EC 1.2.1.4, EC         1.2.1.5, or EC 1.2.1.48.     -   13. The method of embodiment 11, wherein said CoA ligase is         classified under EC 6.2.1.-, such as EC 6.2.1.5 or EC 6.2.1.15.     -   14. The method of embodiment 11, wherein said trans-2-enoyl-CoA         reductase is classified under EC 1.3.1.38, EC 1.3.1.44, or EC         1.3.1.8.     -   15. The method of embodiment 11, wherein said thioesterase is         classified under EC 3.1.2.-.     -   16. The method of embodiment 11, wherein said alcohol         dehydrogenase is classified under EC 1.1.1.-, such as EC         1.1.1.61 or EC 1.1.1.258.     -   17. The method of embodiment 11, wherein said aldehyde         dehydrogenase is classified under EC 1.2.1.3, EC 1.2.1.16, EC         1.2.1.20, EC 1.2.1.24, EC 1.2.1.63, or EC 1.2.1.79, wherein said         aldehyde dehydrogenase classified under EC 1.2.1.16, EC         1.2.1.24, or EC 1.2.1.79 is a succinate-semialdehyde         dehydrogenase, wherein said aldehyde dehydrogenase classified         under EC 1.2.1.20 is a 5-oxopentanoate dehydrogenase, wherein         said aldehyde dehydrogenase classified under EC 1.2.1.63 is a         6-oxohexanoate dehydrogenase, and wherein said aldehyde         dehydrogenase classified under EC 1.2.1.- is a 7-oxoheptanoate         dehydrogenase.     -   18. The method of embodiment 9, wherein said non-3-enal is         converted to azelaic acid using one or more polypeptides having         the enzymatic activities of an enoate reductase, an aldehyde         dehydrogenase, a monooxygenase, and/or an alcohol dehydrogenase.     -   19. The method of embodiment 18, wherein said aldehyde         dehydrogenase is classified under EC 1.2.1.3, EC 1.2.1.4, EC         1.2.1.5, or EC 1.2.1.48.     -   20. The method of embodiment 18, wherein said alcohol         dehydrogenase is classified under EC 1.1.1.-, such as EC         1.1.1.61 or EC 1.1.1.258.     -   21. The method of embodiment 18, wherein said aldehyde         dehydrogenase is classified under EC 1.2.1.3, EC 1.2.1.16, EC         1.2.1.20, EC 1.2.1.24, EC 1.2.1.63, or EC 1.2.1.79, wherein said         aldehyde dehydrogenase classified under EC 1.2.1.16, EC         1.2.1.24, or EC 1.2.1.79 is a succinate-semialdehyde         dehydrogenase, wherein said aldehyde dehydrogenase classified         under EC 1.2.1.20 is a 5-oxopentanoate dehydrogenase, wherein         said aldehyde dehydrogenase classified under EC 1.2.1.63 is a         6-oxohexanoate dehydrogenase and wherein said aldehyde         dehydrogenase classified under EC 1.2.1.- is a 7-oxoheptanoate         dehydrogenase.     -   22. The method of embodiment 9, wherein said 9-oxononanoate is         converted to azelaic acid using a polypeptide having the         enzymatic activity of an aldehyde dehydrogenase.     -   23. The method of embodiment 22, wherein said aldehyde         dehydrogenase is classified under EC 1.2.1.3, EC 1.2.1.16, EC         1.2.1.20, EC 1.2.1.24, EC 1.2.1.63, or EC 1.2.1.79, wherein said         aldehyde dehydrogenase classified under EC 1.2.1.16, EC         1.2.1.24, or EC 1.2.1.79 is a succinate-semialdehyde         dehydrogenase, wherein said aldehyde dehydrogenase classified         under EC 1.2.1.20 is a 5-oxopentanoate dehydrogenase, wherein         said aldehyde dehydrogenase classified under EC 1.2.1.63 is a         6-oxohexanoate dehydrogenase, and wherein said aldehyde         dehydrogenase classified under EC 1.2.1.- is a 7-oxoheptanoate         dehydrogenase.     -   24. The method of any of embodiments 11, 18, or 22, wherein said         azelaic acid is converted to pimeloyl-CoA using one or more         polypeptides having the enzymatic activities of a CoA ligase, an         acyl-CoA dehydrogenase, an enoyl-CoA hydratase, a         3-hydroxyacyl-CoA dehydrogenase, and/or a β-ketothiolase.     -   25. The method of embodiment 24, wherein said CoA ligase is         classified under EC 6.2.1.-.     -   26. The method of embodiment 24, wherein said acyl-CoA         dehydrogenase is classified under EC 1.3.8.-.     -   27. The method of embodiment 26, wherein said acyl-CoA         dehydrogenase is classified under EC 1.3.8.6, EC 1.3.8.7, or EC         1.3.8.8.     -   28. The method of embodiment 24, wherein said enoyl-CoA         hydratase is classified 1E under EC 4.2.1.17 or EC 4.2.1.119.     -   29. The method of embodiment 24, wherein said 3-hydroxyacyl-CoA         delhydrogenase is classified under EC 1.1.1.35, EC 1.1.1.36, or         EC 1.1.1.157.     -   30. The method of embodiment 24, wherein said β-ketothiolase is         classified under EC 2.3.1.16 or EC 2.3.1.174.     -   31. A method for biosynthesizing azelaic acid, said method         comprising enzymatically synthesizing non-3-enal and         9-oxononanoate from 9-hydroxyperoxyoctadec-10,12 dienoate using         a polypeptide having the activity of a hydroperoxide lyase         classified under EC 4.2.99.- and enzymatically converting         non-3renal and/or 9-oxononanoate to azelaic acid.     -   32. The method of embodiment 31, wherein said non-3-enal is         converted to non-3-enoate using a polypeptide having the         activity of an aldehyde dehydrogenase; non-3-enoate is converted         to non-3-enoyl-CoA using a polypeptide having the activity of a         CoA ligase; non-3-enoyl-CoA is converted to non-2-enoyl-CoA         using a polypeptide having the activity of a dodecenoyl-CoA         isomerase; non-2-enoyl-CoA is converted to nonanoyl-CoA using a         polypeptide having the activity of a trans-2-enoyl-CoA         reductase; nonanoyl-CoA is converted to nonanoic acid using a         polypeptide having the activity of a thioesterase; nonanoic acid         is converted to 9-hydroxynonanoic using a polypeptide having the         activity of a monooxygenase; 9-hydroxynonanoic is converted to         9-oxononanoate using a polypeptide having the activity of an         alcohol dehydrogenase; and 9-oxononanoate is converted to         azelaic acid using a polypeptide having the activity of an         aldehyde dehydrogenase.     -   33. The method of embodiment 31, wherein non-3-enal is converted         to nonanal using a polypeptide having the activity of an enoate         reductase; nonanal is converted to nonanoic acid using a         polypeptide having the activity of an aldehyde dehydrogenase;         nonanoic acid is converted to 9-hydroxynonanoic acid using a         polypeptide having the activity of a monooxygenase;         9-hydroxynonanoic acid is converted to 9-oxononanoic acid using         a polypeptide having the activity of an alcohol dehydrogenase;         and 9-oxononanoic acid is converted to azelaic acid using a         polypeptide having the activity of an aldehyde dehydrogenase.     -   34. The method of embodiment 31, wherein said 9-oxononanoate is         converted to azelaic acid using a polypeptide having the         activity of an aldehyde dehydrogenase.     -   35. The method of any one of embodiments 31 to 34, further         comprising the following steps to convert azelaic acid to         pimeloyl-CoA: azelaic acid is converted to azelaoyl-CoA using a         polypeptide having the activity of a CoA ligase; azelaoyl-CoA is         converted to 2,3-dehydro-azelaoyl-CoA using a polypeptide having         the activity of an acyl-CoA dehydrogenase;         2,3-dehydro-azelaoyl-CoA is converted to 3-hydroxy-azelaoyl-CoA         using a polypeptide having the activity of an enoyl-CoA         hydratase; 3′ hydroxy-azelaoyl-CoA is converted to         3-oxo-azelaoyl-CoA using a polypeptide having the activity of a         3-hydroxyacyl-CoA dehydrogenase; and 3-oxo-azelaoyl-CoA is         converted to pimeloyl-CoA using a polypeptide having the         activity of a fl-ketothiolase.     -   36. A method of producing one or more of pimelic acid,         7-aminoheptanoate, 7-hydroxyheptanoate, heptamethylenediamine,         or 1,7-heptanediol, or corresponding salts thereof, said method         comprising the step of converting         9-hydroxyperoxyoctadec-10,12-dienoate to non-3-enal and         9-oxononanoate using a polypeptide having the enzymatic activity         of a hydroperoxide lyase and subsequently converting non-3-enal         or 9-oxononanoate to pimeloyl-CoA.     -   37. The method of embodiment 36, wherein said non-3-enal is         converted to pimeloyl-CoA using an enzymatic pathway comprising         a polypeptide having the activity of a dodecenoyl-CoA isomerase         classified under EC 5.3.3.8 and a polypeptide having the         activity of a monooxygenase classified under EC 1.14.14.- or EC         1.14.15.-.     -   38. The method of embodiment 36, wherein said non-3-enal is         converted to pimeloyl-CoA using an enzymatic pathway comprising         a polypeptide having the activity of an enoate reductase         classified under EC 1.3.1.31 and a polypeptide having the         activity of a monooxygenase classified under EC 1.14.14.- or EC         1.14.15.-.     -   39. The method of embodiment 36, wherein said pimeloyl-CoA is         converted to pimelate semialdehyde using one or more         polypeptides having the activity of an acetylating aldehyde         dehydrogenase.     -   40. The method of embodiment 39, wherein said pimeloyl-CoA is         converted to pimelate semialdehyde using one or more         polypeptides having at least 70%, at least 80%, or at least 85%         sequence identity to an acetylating aldehyde dehydrogenase         encoded by pduB from Salmonella typhimurium or encoded by pduP         from Klebsiella pneumoniae.     -   41. The method of embodiment 36, wherein said pimelate is         converted to pimelate semialdehyde using one or more         polypeptides having the activity of a carboxylate reductase         classified under EC 1.2.99.6.     -   42. The method of embodiment 41, wherein said one or more         polypeptides have at least 70%, at least 80%, or at least 85%         sequence identity to a polypeptide having the activity of a         carboxylate reductase classified under EC 1.2.99.6.     -   43. The method of embodiment 36, wherein said pimeloyl-CoA is         converted to one or more of pimelic acid, 7-aminoheptanoate,         7-hydroxyheptanoate, heptamethylenediamine, or 1,7-heptanediol,         or corresponding salts thereof, in one or more steps.     -   44. The method of embodiment 43, wherein said pimeloyl-CoA is         converted to pimelic acid using at least one polypeptide having         the enzymatic activity of a thioesterase encoded by any one of         yciA from Escherichia coli, acot13 from Mus musculus, or tesB         from Escherichia coli.     -   45. The method of embodiment 44, wherein said pimeloyl-CoA is         converted to pimelic as acid using a polypeptide having at least         70%, at least 80%, or at least 85% sequence identity to a         polypeptide encoded by any one of yciA from Escherichia coli,         acot13 from Mus musculus or tesB from Escherichia coli.     -   46. The method of embodiment 43, wherein said pimeloyl-CoA is         converted to pimelic acid using a polypeptide having the         activity of a CoA ligase classified under EC 6.2.1.- or a         polypeptide having the activity of a CoA transferase classified         under EC 2.8.3.-.     -   47. The method of embodiment 46, wherein said pimeloyl-CoA is         converted to pimelic acid using a polypeptide having at least         70%, at least 80%, or at least 85% sequence identity to a CoA         ligase classified under EC 6.2.1.- or at least 70%, at least         80%, or so at least 85% sequence identity to a CoA transferase         classified under EC 2.8.3.-.     -   48. The method of embodiment 39 or 40, wherein said pimelate         semialdehyde is converted to pimelic acid using one or more         polypeptides having the activity of an aldehyde dehydrogenase         classified under EC 1.2.1.3, EC 1.2.1.16, EC 1.2.1.20, EC         1.2.1.24, EC 1.2.1.63, or EC 1.2.1.79, wherein said aldehyde         dehydrogenase classified under EC 1.2.1.16, EC 1.2.1.24, or EC         1.2.1.79 is a succinate-semialdehyde dehydrogenase, wherein said         aldehyde dehydrogenase classified under EC 1.2.1.20 is a         5.-oxopentanoate dehydrogenase, wherein said aldehyde         dehydrogenase classified under EC 1.2.1.63 is a 6-oxohexanoate         dehydrogenase and wherein said aldehyde dehydrogenase classified         under EC 1.2.1.- is a 7-oxoheptanoate dehydrogenase.     -   49. The method of embodiment 48, wherein said pimelate         semialdehyde is converted to pimelic acid using one or more         polypeptides having at least 70%, at least 80%, or at least 85%         sequence identity to an aldehyde dehydrogenase classified under         EC 1.2.1.3, EC 1.2.1.16, EC 1.2.1.20, EC 1.2.1.24, EC 1.2.1.63,         or EC 1.2.1.79.     -   50. The method of any one of embodiments 39 to 41, wherein said         pimelate semialdehyde is converted to 7-aminoheptanoate using         one or more polypeptides having the activity of a ω-transaminase         classified under EC 2.6.1.-.     -   51. The method of embodiment 50, wherein said pimelate         semialdehyde is converted to 7-aminoheptanoate using one or more         polypeptides having at least 70%, at least 80%, or at least 85%         sequence identity to a polypeptide having the activity of a         ω-transaminase classified under EC 2.6.1.-.     -   52. The method of any one of embodiments 39 to 41, wherein said         pimelate semialdehyde is converted to 7-hydroxyheptanoate using         one or more polypeptides having the enzymatic activity of an         alcohol dehydrogenase, wherein said alcohol dehydrogenase is a         4-hydroxybutanoate dehydrogenase, a 5-hydroxypentanoate         dehydrogenase, or a 6-hydroxyhexanoate dehydrogenase.     -   53. The method of embodiment 52, wherein said alcohol         dehydrogenase is encoded by any one of chnD from Acinetobacter         sp. NCIMB9871, cpnD from Comamonas sp., or gabD from Escherichia         coli.     -   54. The method of embodiment 53, wherein said alcohol         dehydrogenase is encoded by a polypeptide having at least 70%,         at least 80%, or at least 85% sequence identity to a polypeptide         encoded by any one chnD from Acinetobacter sp. NCIMB9871, cpnD         from Comamonas sp., or gabD from Escherichia coli.     -   55. The method of embodiment 50 or 51, wherein said         7-aminoheptanoate is converted to 7-aminoheptanal using one or         more polypeptides having the activity of a carboxylase reductase         classified under EC 1.2.99.6, and wherein said 7-aminoheptanal         is converted to heptamethylenediamine using one or more         polypeptides having the activity of a ω-transaminase classified         under EC 2.6.1.-.     -   56. The method of embodiment 55, wherein said carboxylase         reductase classified under EC 1.2.99.6 is encoded by griC or         griD from Streptomyces griseus.     -   57. The method of embodiment 56, wherein said carboxylase         reductase classified under EC 1.2.99.6 is a polypeptide having         at least 70%, at least 80%, or at least 85% sequence identity to         a polypeptide encoded by griC or griD from Streptomyces 2         griseus.     -   58. The method of embodiment 55, wherein said 7-aminoheptanal is         converted to heptamethylenediamine using one or more         polypeptides having at least 70%, at least 80%, or at least 85%         sequence identity to a polypeptide having the activity of a         co-transaminase classified under EC 2.6.1.-.     -   59. The method of embodiment 50 or 51, wherein said         7-aminoheptanoate is converted to N7-acetyl-7-aminoheptanoate         using one or more polypeptides having the activity of an         N-acetyltransferase classified under EC 2.3.1.32; wherein         N7-acetyl-7-aminoheptanoate is converted to         N7-acetyl-7-aminoheptanal using one or more polypeptides having         the activity of a carboxylase reductase classified under EC         1.2.99.6; wherein N7-acetyl-7-aminoheptanal is converted to         N7-acetyl-1,7-diaminoheptane using one or more polypeptides         having the activity of a ω-transaminase classified under EC         2.6.1.-; and wherein N7-acetyl-1,7-diaminoheptane is converted         to heptamethylenediamine using one or more polypeptides having         the activity of a deacylase classified under EC 3.5.1.-.     -   60. The method of any one of embodiments 52 to 54, wherein said         7-hydroxyheptanoate is converted to 7-hydroxyheptanal using one         or more polypeptides having the activity of a carboxylase         reductase classified under EC 1.2.99.6; wherein         7-hydroxyheptanal is converted to 7-aminoheptanol using one or         more polypeptides having the activity of a ω-transaminase         classified under EC 2.6.1.18, EC 2.6.1.19, or EC 2.6.1.48;         wherein 7-aminoheptanol is converted to 7-aminoheptanal using         one or more polypeptides having the activity of an alcohol         dehydrogenase classified under EC 1.1.1.-; and wherein said         7-aminoheptanal is converted to heptamethylenediamine using one         or more polypeptides having the activity of a ω-transaminase         classified under EC 2.6.1.-.     -   61. The method of embodiment 60, wherein said alcohol         dehydrogenase has at least 70%, at least 80%, or at least 85%         sequence identity to a polypeptide encoded by yqhD from         Escherichia coli.     -   62. The method of embodiment 61, wherein said alcohol         dehydrogenase has at least 70% sequence identity to a         polypeptide encoded by yqhD from Escherichia coli.     -   63. The method of any one of embodiments 39 to 41, wherein said         pimelate semialdehyde is converted to heptanedial using one or         more polypeptides having the activity of a carboxylase reductase         classified under EC 1.2.99.6; wherein heptanedial is converted         to 7-aminoheptanal using one or more polypeptides having as the         activity of a ω-transaminase classified under EC 2.6.1.18, EC         2.6.1.19, EC 2.6.1.48, EC 2.6.1.29, or EC 2.6.1.82; and wherein         7-aminoheptanal is converted to heptamethylenediamine using one         or more polypeptides having the activity of a ω-transaminase         classified under EC 2.6.1.-.     -   64. The method of any of embodiments 52 to 54, wherein said         7-hydroxyheptanoate is converted to 7-hydroxyheptanal using a         carboxylase reductase classified under EC 1.2.99.6; and wherein         7-hydroxyheptanal is converted to 1,7 heptanediol using one more         polypeptides having the activity of an alcohol dehydrogenase         classified under EC 1.1.1.-.     -   65. The method of embodiment 1, wherein said         9-hydroxyperoxyoctadec-10,12 dienoate is enzymatically produced         from octadecanoyl-CoA.     -   66. The method of embodiment 65, wherein said         9-hydroxyperoxyoctadec-10,12-dienoate is enzymatically produced         from octadecanoyl-CoA using one or more polypeptides having the         activity of a delta9-desaturase, a delta12-desaturase, a         thioesterase, and/or a 9-lipoxygenase.     -   67. The method of embodiment 66, wherein said polypeptide having         the activity of a stearoyl-CoA delta9-desaturase is classified         under EC 1.14.19.1.     -   68. The method of embodiment 66, wherein said polypeptide having         the activity of a delta12-desaturase is classified under EC         1.14.19.6.     -   69. The method of embodiment 66, wherein said polypeptide having         the activity of a thioesterase is classified under EC 3.1.2.-.     -   70. The method of embodiment 66, wherein said polypeptide having         the activity of a 98 lipoxygenase is classified under EC         1.13.11.58, EC 1.13.11.60, EC 1.13.11.61, or EC 1.13.11.62.     -   71. The method of any of the preceding embodiments, wherein said         method is performed in a recombinant microorganism.     -   72. The method of embodiment 71, wherein said microorganism is         subjected to a cultivation strategy under aerobic, anaerobic or         micro-aerobic cultivation conditions.     -   73. The method of embodiment 71 or 72, wherein said         microorganism is cultured under so conditions of nutrient         limitation.     -   74. The method according to any one of embodiments 71 to 73,         wherein said microorganism is retained using a ceramic membrane         to maintain a high cell density during fermentation.     -   75. The method of any one of embodiments 71 to 74, wherein the         principal carbon source fed to the fermentation derives from a         biological feedstock.     -   76. The method of embodiment 75, wherein the biological         feedstock is, or derives from, monosaccharides, disaccharides,         lignocellulose, hemicellulose, cellulose, lignin, levulinic         acid, formic acid, triglycerides, glycerol, fatty acids,         agricultural waste, condensed distillers' solubles, plant oils,         or municipal waste.     -   77. The method of any one of embodiments 71 to 74, wherein the         principal carbon source fed to the fermentation derives from a         non-biological feedstock.     -   78. The method of embodiment 77, wherein the non-biological         feedstock is, or derives from, natural gas, syngas, CO₂/H₂,         methanol, ethanol, benzoate, non-volatile residue (NVR) caustic         wash waste stream from cycloheptane oxidation processes, or         terephthalic acid/isophthalic acid mixture waste streams.     -   79. The method of embodiment 71, wherein the microorganism is a         prokaryote.     -   80. The method of embodiment 79, wherein said prokaryote is from         a genus selected from Escherichia, Clostridia, Corynebacteria,         Cupriavidus, Pseudomonas, Delftia, Bacillus, Lactobacillus,         Lactococcus, and Rhodococcus.     -   81. The method of embodiment 80, wherein said prokaryote is         selected from Escherichia coli, Clostridium ljungdahlii,         Clostridium autoethanogenum, Clostridium kluyveri,         Corynebacterium glutamicum, Cupriavidus necator, Cupriavidus         metallidurans. Pseudomonas fluorescens, Pseudomonas putida,         Pseudomonas oleavorans, Delftia acidovorans, Delftia         acidovorans, Bacillus subtillis, Lactobacillus delbrueckii,         Lactococcus lactis, and Rhodococcus equi.     -   82. The method of embodiment 71, wherein the microorganism is a         eukaryote.     -   83. The method of embodiment 82, wherein said eukaryote is from         a genus selected from Aspergillus, Saccharomyces, Pichia,         Yarrowia, Issatchenkia, Debaryomyces, Arxula, and Kluyveromyces.     -   84. The method of embodiment 83, wherein said eukaryote is         selected from Aspergillus niger, Saccharomyces cerevisiae,         Pichia pastoris, Yarrowia lipolytica, Issathenkia orientalis,         Debaryomyces hansenii, Arxula adenoinivorans, and Kluyveromyces         lactis.     -   85. The method of embodiment 71, wherein the microorganism's         tolerance to high concentrations of a C7 building block is         improved relative to a wild type organism.     -   86. The method of embodiment 71, wherein the microorganism's         tolerance to high concentrations of a C7 building block is         improved relative to a wild type organism through continuous         cultivation in a selective environment.     -   87. The method of embodiment 71, wherein said microorganism         comprises an attenuation to one or more of the following         enzymes: a polyhydroxyalkanoate synthase, an acetyl-CoA         thioesterase, a phosphotransacetylase forming acetate, an         acetate kinase, a lactate dehydrogenase, a menaquinol-fumarate         oxidoreductase, an alcohol dehydrogenase forming ethanol, a         triose phosphate isomerase, a pyruvate decarboxylase, a         glucose-6-phosphate isomerase, an NADH-consuming         transhydrogenase, an NADH-specific glutamate dehydrogenase, an         NADH/NADPH-utilizing glutamate dehydrogenase, a pimeloyl-CoA         dehydrogenase; an acyl-CoA dehydrogenase accepting C7 building         blocks and central precursors as substrates; a butaryl-CoA         dehydrogenase; or an adipyl-CoA synthetase.     -   88. The method of any one of embodiments 71 to 87, wherein said         microorganism overexpresses one or more genes encoding: an         acetyl-CoA synthetase, a 6-phosphogluconate dehydrogenase; a         transketolase; a puridine nucleotide transhydrogenase; a         glyceraldehyde-3P-dehydrogenase; a malic enzyme; a         glucose-6-phosphate dehydrogenase; a glucose dehydrogenase; a         fructose 1,6 diphosphatase; a L-alanine dehydrogenase; a         L-glutamate dehydrogenase; a formate dehydrogenase; a         L-glutamine synthetase; a diamine transporter; a dicarboxylate         transporter; and/or a multidrug transporter.     -   89. A recombinant microorganism comprising at least one         exogenous nucleic acid encoding a polypeptide having the         enzymatic activity of (i) a hydroperoxide lyase, (ii) an         aldehyde dehydrogenase, (iii) a CoA ligase, (iv) a         dodecenoyl-CoA isomerase, (v) a trans-2-enoyl-CoA         reductase, (vi) a thioesterase, (vii) a monooxygenase,         and/or (viii) an alcohol dehydrogenase, said microorganism         producing azelaic acid.     -   90. A recombinant microorganism comprising at least one         exogenous nucleic acid encoding a polypeptide having the         enzymatic activity of (i) a hydroperoxide lyase, (ii) an enoate         reductase, (iii) an aldehyde dehydrogenase, (iv) a         monooxygenase, and/or (v) an alcohol dehydrogenase, said         microorganism producing azelaic acid.     -   91. A recombinant microorganism comprising at least one         exogenous nucleic acid encoding a polypeptide having the         enzymatic activity of (i) a hydroperoxide lyase, and/or (ii) an         aldehyde dehydrogenase, said microorganism producing azelaic         acid.     -   92. The recombinant microorganism of any of embodiments 89 to         91, said microorganism further comprising one or more exogenous         polypeptides having the enzymatic activity of: (i) a CoA         ligase, (ii) an acyl-CoA dehydrogenase, (iii) an enoyl-CoA         hydratase, (iv) a 3-hydroxyacyl-CoA dehydrogenase or a 3-oxoacyl         ACP reductase, and/or (v) a β-ketothiolase, said microorganism         further producing pimeloyl-CoA.     -   93. The recombinant microorganism of embodiment 92, said         microorganism further comprising one or more exogenous         polypeptides having the enzymatic activity of a thioesterase, a         CoA ligase, a CoA transferase, an acetylating aldehyde         dehydrogenase, and/or an aldehyde dehydrogenase, said         microorganism further producing pimelic acid.     -   94. The recombinant microorganism of embodiment 92 or 93, said         microorganism further comprising one or more polypeptides having         the activity of an aldehyde 12 dehydrogenase and/or a         ω-transaminase, said microorganism further producing         7-aminoheptanoate.     -   95. The recombinant microorganism of embodiment 92 or 93, said         microorganism further comprising one or more exogenous         polypeptides having the activity of a carboxylate reductase         and/or a ω-transaminase, said microorganism further producing         7-aminoheptanoate.     -   96. The recombinant microorganism of embodiment 92 or 93, said         microorganism further comprising one or more of the following         exogenous enzymes: a carboxylate reductase, an alcohol         dehydrogenase, or an acetylating aldehyde dehydrogenase, said         microorganism further producing 7-hydroxyheptanoate.     -   97. The recombinant microorganism of any one of embodiments 92         to 96, said microorganism comprising one or more of the         following exogenous enzymes: a carboxylate reductase, a         ω-transaminase, an alcohol dehydrogenase, an         N-acetyltransferase, or a deacylase, said microorganism further         producing heptamethylenediamine.     -   98. The recombinant microorganism of embodiment 92 or 93,         wherein said pimeloyl-CoA or said pimelic acid is converted to         pimelate semialdehyde using an acetylating aldehyde         dehydrogenase encoded by pduB from Salmonella typhimurium or         pduP from Klebsiella pneumoniae or one or more polypeptides         having the activity of a carboxylate reductase classified under         EC 1.2.99.6.     -   99. The recombinant microorganism of embodiment 98, said         microorganism comprising polypeptides having the activity of a         carboxylate reductase and one or more ω-transaminases, said         microorganism producing heptamethylenediamine.     -   100. The recombinant microorganism of embodiment 96, said         microorganism further comprising polypeptides having the         activity of a carboxylate reductase and an alcohol         dehydrogenase, said microorganism further producing 1,7         heptanediol.     -   101. The recombinant microorganism of any one of embodiments 89         to 100, said microorganism further comprising one or more         exogenous enzymes: a delta9-desaturase, a delta12-desaturase, a         thioesterase, or a 9-lipoxygenase.     -   102. A non-naturally occurring microorganism comprising at least         one exogenous nucleic acid encoding at least one polypeptide         having the activity of at least one enzyme, at least one         substrate, and at least one product, depicted in any one of FIG.         1 to 7.     -   103. A nucleic acid construct or expression vector comprising a         polynucleotide encoding a polypeptide having carboxylate         reductase activity, wherein the polynucleotide is operably         linked to one or more heterologous control sequences that direct         production of the polypeptide and wherein the polypeptide having         carboxylate reductase activity is selected from: (a) a         polypeptide having at least 70% sequence identity to the         polypeptide of SEQ ID NO: 1; (b) a polypeptide having at least         70% sequence identity to the polypeptide of SEQ ID NO: 2; (c) a         polypeptide having at least 70% sequence identity to the         polypeptide of SEQ ID NO: 3; (d) a polypeptide having at least         70% sequence identity to the polypeptide of SEQ ID NO: 4, (e) a         polypeptide having at least 70% sequence identity to the         polypeptide of SEQ ID NO: 5 and (f) a polypeptide having at         least 70% sequence identity to the polypeptide of SEQ ID NO: 6.     -   104. A nucleic acid construct or expression vector comprising a         polynucleotide encoding a polypeptide having ω-transaminase         activity, wherein the polynucleotide is operably linked to one         or more heterologous control sequences that direct production of         the polypeptide and wherein the polypeptide having         ω-transaminase activity is selected from: (a) a polypeptide         having at least 70% sequence identity to the polypeptide of SEQ         ID NO: 7; (b) a polypeptide having at least 70% sequence         identity to the polypeptide of SEQ ID NO: 8; (c) a polypeptide         having at least 70% sequence identity to the polypeptide of SEQ         ID NO: 9; (d) a polypeptide having at least 70% sequence         identity to the polypeptide of SEQ ID NO: 10; (e) a polypeptide         having at least 70% sequence identity to the polypeptide of SEQ         ID NO: 11 or SEQ ID NO: 48; and (f) a polypeptide having at         least 70% sequence identity to the polypeptide of SEQ ID NO: 12.     -   105. A composition comprising the nucleic acid construct or         expression vector of embodiment 103 or 104.     -   106. A culture medium comprising the nucleic acid construct or         expression vector of embodiment 103 or 104.     -   107. A non-naturally occurring biochemical network comprising a         9-hydroxyperoxyoctadec-10,12-dienoate, an exogenous nucleic acid         encoding a polypeptide having the activity of a hydroperoxide         lyase classified under EC 4.2.99.-, and non-3-enal and         9-oxononanoate.     -   108. A non-naturally occurring biochemical network comprising         non-3-enoyl-CoA, an exogenous nucleic acid encoding a         polypeptide having the activity of a dodecenoyl-CoA isomerase         classified under EC 5.3.3.8 and non-2-enoyl-CoA.     -   109. A non-naturally occurring biochemical network comprising         non-3-enal, an exogenous nucleic acid encoding a polypeptide         having the activity of an enoate reductase classified under EC         1.3.1.31 and nonanal.     -   110. A non-naturally occurring biochemical network comprising         nonanoic acid, an exogenous nucleic acid encoding a polypeptide         having the activity of a monooxygenase classified under EC         1.14.14.- or EC 1.14.15.- and 9-hydroxynonanoic acid.     -   111. Means for producing pimeloyl-CoA, comprising culturing a         non-naturally occurring microorganism comprising at least one         exogenous nucleic acid encoding a polypeptide having the         enzymatic activity of (i) a hydroperoxide lyase, (ii) an         aldehyde dehydrogenase, (iii) a CoA ligase, (iv) a         dodecenoyl-CoA isomerase, (iv) a trans-2-enoyl-CoA         reductase, (v) a thioesterase, (vi) an enoate reductase, (vii) a         monooxygenase, (viii) an alcohol dehydrogenase, (ix) an acyl-CoA         dehydrogenase, (x) an enoyl-CoA hydratase, (xi) a         3-hydroxyacyl-CoA dehydrogenase and (xii) a f-ketothiolase,         expressed in a sufficient amount in said microorganism to         produce pimeloyl-CoA.     -   112. A bio-derived, bio-based, or fermentation-derived product,         wherein said product comprises:         -   (i) a composition comprising at least one bio-derived,             bio-based, or fermentation-derived compound according to any             one of embodiments 6-8, 36, or 39 or any combination             thereof,         -   (ii) a bio-derived, bio-based, or fermentation-derived             polymer comprising the bio-derived, bio-based or             fermentation-derived composition or compound of (i), or any             combination thereof,         -   (iii) a bio-derived, bio-based, or fermentation-derived             resin comprising the bio-derived, bio-based, or             fermentation-derived compound or bio-derived, bio-based, or             fermentation-derived composition of (i) or any combination             thereof or the bio-derived, bio-based, or             fermentation-derived polymer of (ii) or any combination             thereof,         -   (iv) a molded substance obtained by molding the bio-derived,             bio-based, or fermentation-derived polymer of (ii) or the             bio-derived, bio-based, or fermentation-derived resin of             (iii), or any combination thereof,         -   (v) a bio-derived, bio-based, or fermentation-derived             formulation comprising the bio-derived, bio-based, or             fermentation-derived composition of (i), bio-derived,             bio-based, or fermentation-derived compound of (i),             bio-derived, bio-based, or fermentation-derived polymer of             (ii), bio-derived, bio-based, or fermentation-derived resin             of (iii), or bio-derived, bio-based, or fermentation-derived             molded substance of (v), or any combination thereof, or         -   (vi) a bio-derived, bio-based, or fermentation-derived             semi-solid or a non-semi-solid stream, comprising the             bio-derived, bio-based, or fermentation-derived composition             of (i), bio-derived, bio-based, or fermentation-derived             compound of (i), bio-derived, bio-based, or             fermentation-derived polymer of (ii), bio-derived,             bio-based, or fermentation-derived resin of (iii),             bio-derived, bio-based, or fermentation-derived formulation             of (v), or bio-derived, bio-based, or fermentation-derived             molded substance of (iv), or any combination thereof.

Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention pertains. Although methods and materials similar or equivalent to those described herein can be used to practice the invention, suitable methods and materials are described below. All publications, patent applications, patents, and other references mentioned herein are incorporated by reference in their entirety. In case of conflict, the present specification, including definitions, will control. In addition, the materials, methods, and examples are illustrative only and not intended to be limiting.

The details of one or more embodiments of the invention are set forth in the accompanying drawings and the description below. Other features, objects, and advantages of the invention will be apparent from the application, including the written description and drawings, and the claims. The word “comprising” in the claims may be replaced by “consisting essentially of” or with “consisting of,” according to standard practice in patent law.

DESCRIPTION OF DRAWINGS

FIG. 1 is a schematic of exemplary biochemical pathways leading to pimeloyl-CoA via isomerase activity using octadecanoyl-CoA as a central metabolite.

FIG. 2 is a schematic of further exemplary biochemical pathways leading to pimeloyl-CoA via enoate reductase activity using octadecanoyl-CoA as a central metabolite.

FIG. 3 is a schematic of exemplary biochemical pathways leading to pimelic acid using pimeloyl-CoA as a central precursor.

FIG. 4 is a schematic of exemplary biochemical pathways leading to 7-aminoheptanoate using pimeloyl-CoA and pimelate as central precursors.

FIG. 5 is a schematic of exemplary biochemical pathways leading to heptamethylenediamine using 7-aminoheptanoate, 7-hydroxyheptanoate, and pimelate semialdehyde as central precursors.

FIG. 6 is a schematic of exemplary biochemical pathways leading to 7-hydroxyheptanoate using pimeloyl-CoA and pimelate as central precursors.

FIG. 7 is a schematic of an exemplary biochemical pathway leading to 1,7-heptanediol using 7-hydroxyheptanoate as a central precursor.

FIG. 8 contains the amino acid sequences of a Mycobacterium marinum carboxylate reductase (see GenBank Accession No. ACC40567.1, SEQ ID NO: 1), a Mycobacterium smegmatis carboxylate reductase (see GenBank Accession No. ABK71854.1, SEQ ID NO: 2), a Segniliparus rugosus carboxylate reductase (see GenBank Accession No. EFV11917.1, SEQ ID NO: 3), a Mycobacterium smegmatis carboxylate reductase (see GenBank Accession No. ABK75684.1, SEQ ID NO: 4), a Mycobacterium massiliense carboxylate reductase (see GenBank Accession No. EIV11143.1, SEQ ID NO: 5), a Segniliparus rotundus carboxylate reductase (see GenBank Accession No. ADG98140.1, SEQ ID NO: 6), a Chromobacterium violaceum ω-transaminase (see GenBank Accession No. AAQ59697.1, SEQ ID NO: 7), a Pseudomonas aeruginosa ω-transaminase (see GenBank Accession No. AAG08191.1, SEQ ID NO: 8), a Pseudomonas syringae ω-transaminase (see GenBank Accession No. AAY39893.1, SEQ ID NO: 9), a Rhodobacter sphaeroides ω-transaminase (see GenBank Accession No. ABA81135.1, SEQ ID NO: 10), an Escherichia coli ω-transaminase (see GenBank Accession No. AAA57874.1, SEQ ID NO: 11, SEQ ID NO: 48), a Vibrio fluvialis ω-transaminase (see GenBank Accession No. AEA39183.1, SEQ ID NO: 12), a Cucumis sativus hydroperoxide lyase (see GenBank Accession No. AAF64041.1, SEQ ID NO: 13), a Oryza sativa hydroperoxide lyase (see GenBank Accession No. BAG97978.1, SEQ ID NO: 14), a Lactobacillus casei enoate reductase (see GenBank Accession No. AGP69310.1, SEQ ID NO: 15), a Pseudomonas putida enoate reductase (see GenBank Accession No. AAN66878.1, SEQ ID NO: 16), a Saccharomyces cerevisiae isomerase (see GenBank Accession No. AAC83700.1, SEQ ID NO: 17), a Clostridium perfringens thioesterase (see GenBank Accession ABG82470.1, SEQ ID NO: 18), a Saccharomyces cerevisiae isomerase (see GenBank Accession No. AAC83700.1, SEQ ID NO: 19), a Bacteroides thetaiotaomicron thioesterase (see GenBank Accession No. AAO77182.1, SEQ ID NO: 20), a Geobacillus stearothermophilus alcohol dehydrogenase (see GenBank Accession No. CAA81612.1, SEQ ID NO: 21), a Lactobacillus plantarum WCFS1 thioesterase (see GenBank Accession No. CCC78182.1, SEQ ID NO: 22), and an Anaerococcus tetradius ATCC 35098 thioesterase (see GenBank Accession No. EE182564.1, SEQ ID NO: 23). In addition, gene ID and gene sequences (SEQ ID NOs: 24-46) corresponding to the amino acid sequences are provided in FIG. 8.

FIG. 9 is a bar graph summarizing the change in absorbance at 340 nm after 20 minutes, which is a measure of the consumption of NADPH and activity of six carboxylate reductase preparations in enzyme only controls (no substrate).

FIG. 10 is a bar graph of the change in absorbance at 340 nm after 20 minutes, which is a measure of the consumption of NADPH and the activity of two carboxylate reductase preparations for converting pimelate to pimelate semialdehyde relative to the empty vector control.

FIG. 11 is a bar graph of the change in absorbance at 340 nm after 20 minutes, which is a measure of the consumption of NADPH and the activity of six carboxylate reductase preparations for converting 7-hydroxyheptanoate to 7-hydroxyheptanal relative to the empty vector control.

FIG. 12 is a bar graph of the change in absorbance at 340 nm after 20 minutes, which is a measure of the consumption of NADPH and the activity of three carboxylate reductase preparations for converting N7-acetyl-7-aminoheptanoate to N7-acetyl-7-aminoheptanal relative to the empty vector control.

FIG. 13 is a bar graph of the change in absorbance at 340 nm after 20 minutes, which is a measure of the consumption of NADPH and activity of a carboxylate reductase preparation for converting pimelate semialdehyde to heptanedial relative to the empty vector control.

FIG. 14 is a bar graph summarizing the percent conversion of pyruvate to L-alanine (mol/mol) as a measure of the ω-transaminase activity of the enzyme only controls (no substrate).

FIG. 15 is a bar graph of the percent conversion after 4 hours of pyruvate to L-alanine (mol/mol) as a measure of the ω-transaminase activity of four ω-transaminase preparations for converting 7-aminoheptanoate to pimelate semialdehyde relative to the empty vector control.

FIG. 16 is a bar graph of the percent conversion after 4 hours of L-alanine to pyruvate (mol/mol) as a measure of the cg-transaminase activity of three ω-transaminase preparations for converting pimelate semialdehyde to 7-aminoheptanoate relative to the empty vector control.

FIG. 17 is a bar graph of the percent conversion after 4 hours of pyruvate to L-alanine (mol/mol) as a measure of the ω-transaminase activity of six ω-transaminase preparations for converting heptamethylenediamine to 7-aminoheptanal relative to the empty vector control.

FIG. 18 is a bar graph of the percent conversion after 4 hours of pyruvate to L-alanine (mol/mol) as a measure of the ω-transaminase activity of six ω-transaminase preparations for converting N7-acetyl-1,7-diaminoheptane to N7-acetyl-7-aminoheptanal relative to the empty vector control.

FIG. 19 is a bar graph of the percent conversion after 4 hours of pyruvate to L-alanine (mol/mol) as a measure of the ω-transaminase activity of three r-transaminase preparations for converting 7-aminoheptanol to 7-oxoheptanol relative to the empty vector control.

DETAILED DESCRIPTION

In general, this document provides enzymes, non-natural pathways, cultivation strategies, feedstocks, microorganisms, and attenuations to the microorganism's biochemical network, for producing pimeloyl-CoA or one or more of pimelic acid, 7-aminoheptanoate, 7-hydroxyheptanoic acid, heptamethylenediamine, or 1,7-heptanediol, or corresponding salts thereof, all of which are referred to as C7 building blocks herein.

As used herein, a “bio-based product” is a product in which both the feedstock (e.g., sugars from sugar cane, corn, wood; biomass; waste streams from agricultural processes) and the conversion process to the product are biologically based (e.g., fermentation/enzymatic transformation involving a biological host/organism/enzyme). As used herein, a “bio-derived product” is a product in which one of the feedstocks (e.g., sugars from sugar cane, corn, wood; biomass; waste streams from agricultural processes) or the conversion process to the product is biologically based (e.g., fermentation/enzymatic transformation involving a biological host/organism/enzyme).

As used herein, a “fermentation-derived product” is a product produced by fermentation involving a biological host or organism.

The term “C7 building block” is used to denote a seven (7) carbon chain aliphatic backbone. As used herein, the term “central precursor” is used to denote any metabolite in any metabolic pathway shown herein leading to the synthesis of a C7 building block. The term “central metabolite” is used herein to denote a metabolite that is produced in all microorganisms to support growth.

Microorganisms described herein can include endogenous pathways that can be manipulated such that pimeloyl-CoA or one or more other C7 building blocks can be produced. In an endogenous pathway, the microorganism naturally expresses all of the enzymes catalyzing the reactions within the pathway. A microorganism containing an engineered pathway does not naturally express all of the enzymes catalyzing the reactions within the pathway but has been engineered such that all of the enzymes within the pathway are expressed in the microorganism.

The term “exogenous” as used herein with reference to a nucleic acid (or a protein) and a microorganism refers to a nucleic acid that does not occur in (and cannot be obtained from) a cell of that particular type as it is found in nature or a protein encoded by such a nucleic acid. Thus, a non-naturally-occurring nucleic acid is considered to be exogenous to a microorganism once in the microorganism. It is important to note that non-naturally-occurring nucleic acids can contain nucleic acid subsequences or fragments of nucleic acid sequences that are found in nature provided the nucleic acid as a whole does not exist in nature. For example, a nucleic acid molecule containing a genomic DNA sequence within an expression vector is a non-naturally-occurring nucleic acid, and thus is exogenous to a microorganism once introduced into the microorganism, since that nucleic acid molecule as a whole (genomic DNA plus vector DNA) does not exist in nature. Thus, any vector, autonomously replicating plasmid, or virus (e.g., retrovirus, adenovirus, or herpes virus) that as a whole does not exist in nature is considered to be non-naturally-occurring nucleic acid. It follows that genomic DNA fragments produced by PCR or restriction endonuclease treatment as well as cDNAs are considered to be non-naturally-occurring nucleic acid since they exist as separate molecules not found in nature. It also follows that any nucleic acid containing a promoter sequence and polypeptide-encoding sequence (e.g., cDNA or genomic DNA) in an arrangement not found in nature is a non-naturally-occurring nucleic acid. A nucleic as acid that is naturally-occurring can be exogenous to a particular microorganism. For example, an entire chromosome isolated from a cell of yeast x is an exogenous nucleic acid with respect to a cell of yeast y once that chromosome is introduced into a cell of yeast y.

In contrast, the term “endogenous” as used herein with reference to a nucleic acid (e.g., a gene) (or a protein) and a microorganism refers to a nucleic acid (or protein) that does occur in (and can be obtained from) that particular microorganism as it is found in nature. Moreover, a cell “endogenously expressing” a nucleic acid (or protein) expresses that nucleic acid (or protein) as does a microorganism of the same particular type as it is found in nature. Moreover, a microorganism “endogenously producing” or that a “endogenously produces” a nucleic acid, protein, or other compound produces that nucleic acid, protein, or compound as does a microorganism of the same particular type as it is found in nature.

For example, depending on the microorganism and the compounds produced by the microorganism, one or more polypeptides having the following specific enzymatic activities may be expressed in the microorganism in addition to a hydroperoxide lyase: an acetylating aldehyde dehydrogenase, a CoA ligase, a dodecenoyl-CoA isomerase or an enoate reductase, a trans-2-enoyl-CoA reductase, a thioesterase, a monooxygenase, an enoyl-CoA hydratase, a deacetylase, an acyl-CoA dehydrogenase, an enoyl-CoA hydratase, an alcohol dehydrogenase, a 4-hydroxybutanoate dehydrogenase, a 6-hydroxyhexanoate dehydrogenase, an aldehyde dehydrogenase, a succinate-semialdehyde dehydrogenase, a 5-oxopentanoate dehydrogenase, a 6-oxohexanoate dehydrogenase, a 7-oxoheptanoate dehydrogenase, an acyl-CoA dehydrogenase, an enoyl-CoA hydratase, a 3-hydroxyacyl-CoA dehydrogenase, a 3-oxoacyl ACP reductase, a fi-ketothiolase, a CoA transferase, a carboxylate reductase, a ω-transaminase, an N-acetyltransferase, and/or a deacylase. In recombinant microorganisms expressing a polypeptide having the activity of a carboxylate reductase, a polypeptide having the activity of a phosphopantetheinyl transferase also can be expressed as it enhances activity of the carboxylate reductase.

For example, a recombinant microorganism can include a polypeptide having the activity of an exogenous hydroperoxide lyase and produce non-3-enal and 9-oxononanoate from 9-hydroxyperoxyoctadec-10,12-dienoate. The non-3-enal and 9-oxononanoate can be converted enzymatically to pimeloyl-CoA and subsequently to one or more of pimelic acid, 7-aminoheptanoate, 7-hydroxyheptanoic acid, heptamethylenediamine, or 1,7-heptanediol, or corresponding salts thereof.

For example, a recombinant microorganism producing pimeloyl-CoA can include one or more of exogenous polypeptides having the enzymatic activity of: a thioesterase, a CoA ligase, a CoA transferase, an acetylating aldehyde dehydrogenase, a succinate semialdehyde dehydrogenase, a 5-oxopentanoate dehydrogenase, a 6-oxohexanoate dehydrogenase, and/or a 7-oxoheptanoate dehydrogenase, and further produce pimelic acid. See FIG. 3.

For example, a recombinant microorganism producing pimeloyl-CoA can include an exogenous polypeptide having the activity of a thioesterase and produce pimelic acid. For example, a recombinant microorganism producing pimeloyl-CoA can include an exogenous polypeptide having the activity of a CoA ligase or a CoA transferase, and further produce pimelic acid. For example, a recombinant microorganism producing pimeloyl-CoA can include an exogenous polypeptide having the activity of an acetylating aldehyde dehydrogenase and one or more polypeptides having the enzymatic activity of: an aldehyde dehydrogenase, a succinate-semialdehyde dehydrogenase, a 5-oxopentanoate dehydrogenase, a 6-oxohexanoate dehydrogenase, and/or a 7-oxoheptanoate dehydrogenase, and produce pimelic acid. See FIG. 3.

For example, a recombinant microorganism can include one or more exogenous polypeptides having the enzymatic activity of an aldehyde dehydrogenase, a ω-transaminase, and/or a carboxylate reductase, and produce 7-aminoheptanoate. See FIG. 4.

For example, a recombinant microorganism producing pimeloyl-CoA can include an exogenous polypeptide having the activity of an acetylating aldehyde dehydrogenase and an exogenous polypeptide having the activity of a ω-transaminase, and produce 7-aminoheptanoate. For example, a recombinant microorganism producing pimelate (see FIG. 3) can include an exogenous polypeptide having the activity of a carboxylate reductase and an exogenous polypeptide having the activity of a ω-transaminase, and produce 7-aminoheptanoate. See FIG. 4.

For example, a recombinant microorganism producing pimeloyl-CoA can include one or more exogenous polypeptides having the enzymatic activity of a carboxylate reductase, an alcohol dehydrogenase, a 4-hydroxybutanoate dehydrogenase, a 5, hydroxypentanoate dehydrogenase, a 6-hydroxyhexanoate dehydrogenase, and/or an so aldehyde dehydrogenase and further produce 7-hydroxyheptanoate. See FIG. 6.

For example, a recombinant microorganism producing pimeloyl-CoA can include an exogenous polypeptide having the activity of a carboxylate reductase and an exogenous polypeptide having the activity of a 4-hydroxybutanoate dehydrogenase, and produce 7-hydroxyheptanoate. For example, a recombinant microorganism producing pimeloyl-CoA can include an exogenous polypeptide having the activity of a carboxylate reductase and an exogenous polypeptide having the activity of a 5-hydroxypentanoate dehydrogenase, and produce 7-hydroxyheptanoate. For example, a recombinant microorganism producing pimeloyl-CoA can include an exogenous polypeptide having the activity of a carboxylate reductase and an exogenous polypeptide having the activity of a 6-hydroxyhexanoate dehydrogenase, and produce 7-hydroxyheptanoate. For example, a recombinant microorganism producing pimelate (see FIG. 3) can include an exogenous polypeptide having the activity of a carboxylate reductase and an exogenous polypeptide having the activity of either a 4-hydroxybutanoate dehydrogenase, a 5-hydroxypentanoate dehydrogenase, or a 6-hydroxyhexanoate dehydrogenase, and produce 7-hydroxyheptanoate. See FIG. 6.

For example, a recombinant microorganism producing pimeloyl-CoA can include one or more exogenous polypeptides to produce 7-aminoheptanoate or 7-hydroxyheptanoate. See FIG. 4 and FIG. 6. A recombinant microorganism producing 7-aminoheptanoate or 7-hydroxyheptanoate can include one or more exogenous polypeptides having the activity of: a carboxylate reductase, a ω-transaminase, an alcohol dehydrogenase, an N-acetyltransferase, and/or a deacylase, and produce heptamethylenediamine. See FIG. 5.

For example, a recombinant microorganism producing pimeloyl-CoA can include the polypeptides necessary to convert pimeloyl-CoA to 7-aminoheptanoate and can 2 include an exogenous polypeptide having the activity of a carboxylate reductase and one or more exogenous polypeptides having the activity of ω-transaminases (e.g., one transaminase or two different transaminases) and produce heptamethylenediamine. For example, a recombinant microorganism producing pimeloyl-CoA can include the polypeptides necessary to convert pimeloyl-CoA to 7-aminoheptanoate and can include so one or more exogenous polypeptides having the activity of an N-acetyltransferase, a carboxylate reductase, a ω-transaminase, and/or a deacylase, and produce heptamethylenediamine. For example, a recombinant microorganism producing pimeloyl-CoA can include the polypeptides necessary to convert pimeloyl-CoA to 7-hydroxyheptanoate and can include one or more exogenous polypeptides having the 6 activity of a carboxylate reductase, a ω-transaminase (e.g., one transaminase or two different transaminases), and/or an alcohol dehydrogenase, and produce heptamethylenediamine. See FIG. 5.

For example, a recombinant microorganism producing pimeloyl-CoA can include the polypeptides having the necessary enzymatic activity for conversion of pimeloyl-CoA to 7-hydroxyheptanoate (see FIG. 6) as described above and can also include one or more exogenous polypeptides having the enzymatic activity of a carboxylate reductase and/or an alcohol dehydrogenase, and further produce 1,7-heptanediol from 7-hydroxyheptanoate. See FIG. 7.

In any of the recombinant microorganisms, the recombinant microorganism also can include one or more (e.g., one, two, or three) of the following exogenous enzymes used to convert either octadecanoyl-CoA to 9-hydroxyperoxyoctadec-10,12-dienoate: a delta9-desaturase, a delta12-desaturase, a thioesterase, or a 9-lipoxygenase. For example, a recombinant microorganism can include a delta9-desaturase, a delta12-desaturase, a thioesterase, and a 9-lipoxygenase.

Within an engineered pathway, the enzymes can be from a single source, i.e., from one species or genera, or can be from multiple sources, i.e., different species or genera. Nucleic acids encoding the enzymes described herein have been identified from various organisms and are readily available in publicly available databases such as GenBank or EMBL. Enzyme Commission (EC) numbers for many enzymes are also provided. EC numbers are well known in the art and provide a numerical classification scheme for enzymes based on the chemical reactions they catalyze. An enzyme classified with an EC number to the fourth level is discretely and specifically classified on the basis of the reactions that its members are able to perform. Well known nomenclature databases such as ENZYME, maintained by the Swiss Institute of Bioinformatics, so provide examples of specific enzymes corresponding to specific EC numbers.

Any of the enzymes described herein that can be used for production of one or more C7 building blocks can have at least 70% sequence identity (homology) (e.g., at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) to the amino acid sequence of the corresponding wild-type enzyme. It will be appreciated that the sequence identity can be determined on the basis of the mature enzyme (e.g., with any signal sequence removed) or on the basis of the immature enzyme (e.g., with any signal sequence included). It also will be appreciated that the initial methionine residue may or may not be present on any of the enzyme sequences described herein.

For example, a polypeptide having the activity of a carboxylate reductase described herein can have at least 70% sequence identity (homology) (e.g., at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) to the amino acid sequence of a Mycobacterium marinum (see GenBank Accession No. ACC40567.1, SEQ ID NO: 1), a Mycobacterium smegmatis (see GenBank Accession No. ABK71854.1, SEQ ID NO: 2), a Segniliparus rugosus (see GenBank Accession No. EFV11917.1, SEQ ID NO: 3), a Mycobacterium smegmatis (see GenBank Accession No. ABK75684.1, SEQ ID NO: 4), a Mycobacterium massiliense (see GenBank Accession No. EIV11143.1, SEQ ID NO: 5), or a Segniliparus rotundus (see GenBank Accession No. ADG98140.1, SEQ ID NO: 6) carboxylate reductase. See FIG. 8.

For example, a polypeptide having the activity of a ω-transaminase described herein can have at least 70% sequence identity (homology) (e.g., at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) to the amino acid sequence of a Chromobacterium violaceum (see GenBank Accession No. AAQ59697.1, SEQ ID NO: 7), a Pseudomonas aeruginosa (see GenBank Accession No. AAG08191.1, SEQ ID NO: 8), a Pseudomonas syringae (see GenBank Accession No. AAY39893.1, SEQ ID NO: 9), a Rhodobacter sphaeroides (see GenBank Accession No. ABA81135.1, SEQ ID NO: 10), an Escherichia coli (see GenBank Accession No. AAA57874.1, SEQ ID NO: 11, SEQ ID NO: 48), or a Vibrio fluvialis (see GenBank Accession No. AEA39183.1, SEQ ID NO: 12) ω-transaminase. Some of these ω-transaminases are diamine ω-transaminases. See FIG. 8.

For example, a polypeptide having the activity of a hydroperoxide lyase described herein can have at least 70% sequence identity (homology) (e.g., at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) to the amino acid sequence of a Cucumis sativus (see GenBank Accession No. AAF64041.1, SEQ ID NO: 13) or a Oryza sativa hydroperoxide lyase (see GenBank Accession No. BAG97978.1, SEQ ID NO: 14). See FIG. 8.

For example, a polypeptide having the activity of an enoate reductase described herein can have at least 70% sequence identity (homology) (e.g., at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) to the amino acid sequence of a Lactobacillus casei (see GenBank Accession No. AGP69310.1, SEQ ID NO: 15) or a Pseudomonas putida enoate reductase (see GenBank Accession No. AAN66878.1, SEQ ID NO: 16). See FIG. 8.

For example, a polypeptide having the activity of an isomerase described herein can have at least 70% sequence identity (homology) (e.g., at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) to the amino acid sequence of a Saccharomyces cerevisiae isomerase (see GenBank Accession No. AAC83700.1, SEQ ID NO: 17 and SEQ ID NO: 19). See FIG. 8.

For example, a polypeptide having the activity of a thioesterase described herein can have at least 70% sequence identity (homology) (e.g., at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) to the amino acid sequence of a Clostridium perfringens (see GenBank Accession No. ABG82470.1, SEQ ID NO: 18), a Bacteroides thetaiotaomicron VPI-5482 (see GenBank Accession No. AAO77182.1, SEQ ID NO: 20), a Lactobacillus plantarum WCFS1 (see GenBank Accession No. CCC78182.1, SEQ ID NO: 22), or a Anaerococcus tetradius ATCC 35098 (see GenBank Accession No. EEI82564.1, SEQ ID NO: 23). See FIG. 8.

For example, a polypeptide having the activity of an alcohol dehydrogenase described herein can have at least 70% sequence identity (homology) (e.g., at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) to the amino acid sequence of a Geobacillus stearothermophilus (see GenBank Accession No. CAA81612.1, SEQ ID NO: 21). See FIG. 8.

The percent identity (homology) between two amino acid sequences can be determined as follows. First, the amino acid sequences are aligned using the BLAST 2 Sequences (B12seq) program from the stand-alone version of BLASTZ containing BLASTP version 2.0.14. This stand-alone version of BLASTZ can be obtained from Fish & Richardson's web site (e.g., www.fr.com/blast/) or the U.S. government's National Center for Biotechnology Information web site (www.ncbi.nlm.nih.gov). Instructions explaining how to use the B12seq program can be found in the readme file accompanying BLASTZ. B12seq performs a comparison between two amino acid sequences using the BLASTP algorithm. To compare two amino acid sequences, the options of B12seq are set as follows: -i is set to a file containing the first amino acid sequence to be compared (e.g., C:\seq1.txt); -j is set to a file containing the second amino acid sequence to be compared (e.g., C:\seq2.txt); -p is set to blastp; -o is set to any desired file name (e.g., C:\output.txt); and all other options are left at their default setting. For example, the following command can be used to generate an output file containing a comparison between two amino acid sequences: C:\B12seq -i c:\seq1.txt -j c:\seq2.txt -p blastp -o c:\output.txt. If the two compared sequences share homology (identity), then the designated output file will present those regions of homology as aligned sequences. If the two compared sequences do not share homology (identity), then the designated output file will not present aligned sequences. Similar procedures can be following for nucleic acid sequences except that blastn is used.

Once aligned, the number of matches is determined by counting the number of positions where an identical amino acid residue is presented in both sequences. The percent identity (homology) is determined by dividing the number of matches by the length of the full-length polypeptide amino acid sequence followed by multiplying the resulting value by 100. It is noted that the percent identity (homology) value is rounded to the nearest tenth. For example, 78.11, 78.12, 78.13, and 78.14 is rounded down to 78.1, while 78.15, 78.16, 78.17, 78.18, and 78.19 is rounded up to 78.2. It also is noted that the length value will always be an integer.

It will be appreciated that a number of nucleic acids can encode a polypeptide having a particular amino acid sequence. The degeneracy of the genetic code is well known to the art; i.e., for many amino acids, there is more than one nucleotide triplet that serves as the codon for the amino acid. For example, codons in the coding sequence for a given enzyme can be modified such that optimal expression in a particular species (e.g., bacteria or fungus) is obtained, using appropriate codon bias tables for that species.

Functional fragments of any of the enzymes described herein can also be used in the methods of the document. The term “functional fragment” as used herein refers to a peptide fragment of a protein that has at least 25% (e.g., at least: 30%; 40%; 50%; 60%; 70%; 75%; 80%; 85%; 90%; 95%; 98%; 99%; 100%; or even greater than 100%) of the activity of the corresponding mature, full-length, wild-type protein. The functional fragment can generally, but not always, be comprised of a continuous region of the protein, wherein the region has functional activity.

This document also provides (i) functional variants of the enzymes used in the methods of the document and (ii) functional variants of the functional fragments described above. Functional variants of the enzymes and functional fragments can contain additions, deletions, or substitutions relative to the corresponding wild-type sequences. Enzymes with substitutions will generally have not more than 100 (e.g., not more than one, two, three, four, five, six, seven, eight, nine, ten, 12, 15, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90 or 100) amino acid substitutions (e.g., conservative substitutions). This applies to any of the enzymes described herein and functional fragments. A conservative substitution is a substitution of one amino acid for another with similar characteristics. Conservative substitutions include substitutions within the following groups: valine, alanine and glycine; leucine, valine, and isoleucine; aspartic acid and glutamic acid; asparagine and glutamine; serine, cysteine, and threonine; lysine and arginine; and phenylalanine and tyrosine. The nonpolar hydrophobic amino acids include alanine, leucine, isoleucine, valine, proline, phenylalanine, tryptophan and methionine. The polar neutral amino acids include glycine, serine, threonine, cysteine, tyrosine, asparagine and glutamine. The positively charged (basic) amino acids include arginine, lysine and histidine. The negatively charged (acidic) amino acids include aspartic acid and glutamic acid. Any substitution of one member of the above-mentioned polar, basic or acidic groups by another member of the same group can be deemed a conservative substitution. By contrast, a nonconservative substitution is a substitution of one amino acid for another with dissimilar characteristics.

Deletion variants can lack one, two, three, four, five, six, seven, eight, nine, ten, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 40, or 50 amino acid segments (of two or more amino acids) or non-contiguous single amino acids. Additions (addition variants) include fusion proteins containing: (a) any of the enzymes described herein or a fragment thereof; and (b) internal or terminal (C or N) irrelevant or heterologous amino acid sequences. In the context of such fusion proteins, the term “heterologous amino acid sequences” refers to an amino acid sequence other than (a). A heterologous sequence can be, for example a sequence used for purification of the recombinant protein (e.g., FLAG, polyhistidine (e.g., heptahistidine (SEQ ID NO: 47)), hemagglutinin (HA), glutathione-S-transferase (GST), or maltosebinding protein (MBP)). Heterologous sequences also can be proteins useful as detectable markers, for example, luciferase, green fluorescent protein (GFP), or chloramphenicol acetyl transferase (CAT). In some embodiments, the fusion protein contains a signal sequence from another protein. In certain microorganisms (e.g., yeast cells), expression and/or secretion of the target protein can be increased through use of a heterologous signal sequence. In some embodiments, the fusion protein can contain a carrier (e.g., KLH) useful, e.g., in eliciting an immune response for antibody generation) or ER or Golgi apparatus retention signals. Heterologous sequences can be of varying length and in some cases can be a longer sequences than the full-length target proteins to which the heterologous sequences are attached.

Engineered microorganisms can naturally express none or some (e.g., one or more, two or more, three or more, four or more, five or more, or six or more) of the enzymes of the pathways described herein. Thus, a pathway within an engineered microorganism can include all exogenous enzymes, or can include both endogenous and exogenous enzymes. Endogenous genes of the engineered microorganisms also can be disrupted to prevent the formation of undesirable metabolites or prevent the loss of intermediates in the pathway through other enzymes acting on such intermediates. Engineered microorganisms can be referred to as recombinant microorganisms or recombinant cells. As described herein recombinant microorganisms can include nucleic acids encoding one or more of a hydroperoxide lyase, an aldehyde dehydrogenase, a CoA ligase, a dodecenoyl-CoA isomerase or an enoate reductase, a trans-2-enoyl-CoA reductase, a thioesterase, a monooxygenase, an enoyl-CoA hydratase, a deacetylase, an acyl-CoA dehydrogenase, an enoyl-GoA hydratase, an alcohol dehydrogenase, a 4-hydroxybutanoate dehydrogenase, a 6-hydroxyhexanoate dehydrogenase, an aldehyde dehydrogenase, a succinate-semialdehyde dehydrogenase a 5-oxopentanoate dehydrogenase, a 6-oxohexanoate dehydrogenase, a 7-oxoheptanoate dehydrogenase, an acyl-CoA dehydrogenase, an enoyl-CoA hydratase, a 3-hydroxyacyl-CoA dehydrogenase, a 3-oxoacyl ACP reductase, a β-ketothiolase, a delta9-desaturase, a delta12-desaturase, a thioesterase, or a 9-lipoxygenase, as described herein.

In addition, the production of C7 building blocks can be performed in vitro using the isolated enzymes described herein, using a lysate (e.g., a cell lysate) from a microorganism as a source of the enzymes, or using one or more lysates from different microorganisms as the source of the enzymes.

The reactions of the pathways described herein can be performed in one or more microorganisms (a) naturally expressing one or more relevant enzymes, (b) genetically engineered to express one or more relevant enzymes, or (c) naturally expressing one or more relevant enzymes and genetically engineered to express one or more relevant enzymes. Alternatively, relevant enzymes can be isolated, purified or extracted from of the above types of microorganism cells and used in a purified or semi-purified form. Moreover, such extracts include lysates (e.g., cell lysates) that can be used as sources of relevant enzymes. In the methods provided by the document, all the steps can be performed in microorganism cells, all the steps can be performed using extracted enzymes, or some of the steps can be performed in cells and others can be performed using extracted enzymes.

Enzymes Enzymes Generating Pimeloyl-CoA

As depicted in FIG. 1 and FIG. 2, 9-hydroxyperoxyoctadec-10, 12-dienoate can be enzymatically synthesized from the central metabolite octadecanoyl-CoA using one or more exogenous polypeptides having the enzymatic activity of: a delta9-desaturase, a delta12-desaturase, a thioesterase, and/or a 9-lipoxygenase.

In some embodiments, a polypeptide having the activity of a delta9-desaturase may be classified under EC 1.14.19.1, such as, for example, the gene product of Le-FAD1 from Lentinula edodes (UniProtKB Accession No. Q76C19), the gene product of SCD1 from Mesocricetus auratus (UniProtKB Accession No. A7LCI9), an acyl-CoA-delta9-3a-desaturase from Dendrolimus punctatus (UniProtKB Accession No. B7SB75), the gene product of scd1 from Rattus norvegicus (UniProtKB Accession No. P07308), the gene product of PF3D70511200 from Plasmodium falciparum (UniProtKB Accession No. Q8I0W9), or the gene product of desB1 from Bombus lucorum (UniProtKB Accession No. A5CKEI).

A polypeptide having the activity of a delta12-desaturase may be classified under EC 1.14.19.6, such as, for example, the gene product of D12Des from Acheta domesticus (UniProtKB Accession No. B7SB91), the gene product of FAD2 from Gossypium hirsutum (UniProtKB Accession No. Q8W2B9), the gene product of CFad6 from Chlorella vulgaris (UniProtKB Accession No. D3U658), a delta12 fatty acid desaturase from Triadica sebifera (UniProtKB Accession No. A5J295), the gene product of Pc-fad2 from Phanerochaete chrysosporium (UniProtKB Accession No. D4Q8H2), the gene product of Cs-fad2 from Ceriporiopsis subvermispora (UniProtKB Accession No. D4Q8S6), or the gene product of AN1037.2 from Emericella nidulans (UniProtKB Accession No. Q5BEJ3).

A polypeptide having the activity of a thioesterase may be classified under EC 3.1.2.-, such as, for example, the gene product of BT_2075 from Bacteroides thetaiotaomicron (strain ATCC 29148/DSM 2079/NCTC 10582/E50/VPI-5482) (GenBank Accession No. AAO77182.1, SEQ ID NO: 20), the gene product of lp_0708 from Lactobacillus plantarum (strain ATCC BAA-793/NCIMB 8826/WCFS1) (GenBank Accession No. CCC78182.1, SEQ ID NO: 22), the gene product of HMPREF0077_1317 from Anaerococcus tetradius ATCC 35098 (GenBank Accession No. EE182564.1, SEQ ID NO: 23), or the gene product of CPF_2954 from Clostridium perfringens (strain ATCC 13124/DSM 756/JCM 1290/NCIMB 6125/NCTC 8237/Type A) (GenBank Accession No. ABG82470.1, SEQ ID NO: 18).

A polypeptide having the activity of a 9-lipoxygenase may be classified, for example, under EC 1.13.11.58, EC 1.13.11.60, EC 1.13.11.61, or EC 1.13.11.62, such as, for example, an allene oxide synthase-lipoxygenase protein from Plexaura homomalla (UniProtKB Accession No. O16025), a Psi-producing oxygenase A from Emericella nidulans (UniProtKB Accession No. Q6RET3), a 5,8-linoleate dial synthase from Aspergillus fumigatus (UniProtKB Accession No. C1KH66), or a linoleate diol synthase from Gaeunmannomyces graminis (UniProtKB Accession No. Q9UUS2).

As further depicted in FIG. 1 and FIG. 2, 9-hydroxyperoxyoctadec-10,12-dienoate may be enzymatically cleaved into non-3-enal and 9-oxononanoate using a polypeptide having the activity of a hydroperoxide lyase. In some embodiments, a polypeptide having the activity of a hydroperoxide lyase may be classified under EC 4.2.99.-, such as, for example, the gene product of Cucumis sativus (GenBank Accession No. AAF64041.1, SEQ ID NO: 13) or the gene product of Oryza sativa (GenBank Accession No. BAG97978.1, SEQ ID NO: 14).

As shown in FIG. 1 and FIG. 2, non-3-enal and 9-oxononanoate may be converted by separate enzymatic pathways to azelaic acid. Azelaic acid, regardless of its origination from non-3-enal or 9-oxononanoate, may then be converted to pimeloyl-CoA. The enzymes involved in the conversion of non-3-enal to azelaic acid, 9-oxononanoate to azelaic acid and azelaic acid to pimeloyl-CoA are as described in the following paragraphs.

As shown in FIG. 1, non-3-enal may be converted to azelaic acid by one or more exogenous polypeptides having the enzymatic activities of: (i) an aldehyde dehydrogenase, (ii) a CoA ligase, (iii) a dodecenoyl-CoA isomerase, (iv) a trans-2-enoyl-CoA reductase, (v) a thioesterase, (vi) a monooxygenase, (vii) an alcohol dehydrogenase, and/or (viii) a succinate-semialdehyde dehydrogenase, a 5-oxopentanoate dehydrogenase, a 6-oxohexanoate dehydrogenase, and/or a 7-oxoheptanoate dehydrogenase.

As shown in FIG. 2, non-3-enal may be converted to azelaic acid by one or more exogenous polypeptides having the enzymatic activities of: (i) an enal isomerase, (ii) an enoate reductase, (iii) an aldehyde dehydrogenase, (iv) a monooxygenase, (v) an alcohol dehydrogenase, and/or (vi) a succinate-semialdehyde dehydrogenase, a 7-oxoheptanoate dehydrogenase, a 6-oxohexanoate dehydrogenase, and/or a 5-oxopentanoate dehydrogenase.

In some embodiments, a polypeptide having the activity of an aldehyde dehydrogenase may be classified under EC 1.2.1.-, such as EC 1.2.1.3, EC 1.2.1.4, EC 1.2.1.5, or EC 1.2.1.48, such as, for example, the gene product of Bt-aldh from Geobacillus thermoleovorans B23 (UniProtKB Accession No. Q9FAB1), the gene product of dhaS from Bacillus subtilis (UniProtKB Accession No. O34660), the gene product of ALD5 from Saccharomyces cerevisiae (UniProtKB Accession No. A6ZR27), the gene product of ALDH2C4 from Arabidopsis thaliana (UniProtKB Accession No. Q56YU0), the gene product of aldh7 from Rhodococcus ruber (UniProtKB Accession No. Q840S9), the gene product of alkH from Pseudomonas oleovorans (UniProtKB Accession No. P12693), the gene product of ald1 from Acinetobacter sp. M-1 (UniProtKB Accession No. Q9FDS1), or the gene product of acoD from Ralstonia eutropha (UniProtKB Accession No. P46368).

In some embodiments, a polypeptide having the activity of an enoate reductase may be classified, for example, under EC 1.3.1.31, such as, for example, the gene product of xenA from Pseudomonas putida (GenBank Accession No. AAN66878.1, SEQ ID NO: 16) or the gene product of LOCK919_2632 from Lactobacillus casei (GenBank Accession No. AGP69310.1, SEQ ID NO: 15).

In some embodiments, a polypeptide having the activity of a CoA ligase may be classified under EC 6.2.1.-, such as, for example, the gene product of acs6 from Brassica napus (UniProtKB Accession No. Q9FNT6), the gene product of PCS60 from Saccharomyces cerevisiae (UniProtKB Accession No. P38137), the gene product of alkK from Pseudomonas oleovorans (UniProtKB Accession No. Q00594), the gene product of ACSM5 from Homo sapiens (UniProtKB Accession No. Q6NUN0), or the gene product of alkK from Aeropyrum pernix (UniProtKB Accession No. Q9YF45).

In some embodiments, a polypeptide having the activity of a dodecenoyl-CoA isomerase may be classified under EC 5.3.3.8, such as, for example, the gene product of ECI1 from Saccharomyces cerevisiae (GenBank Accession No. AAC83700.1, SEQ ID NO: 17 and SEQ ID NO: 19, Geisbrecht et al J. Biol. Chem, 1998 273 (50) 33184-33191).

In some embodiments, a polypeptide having the activity of a trans-2-enoyl-CoA reductase may be classified under EC 1.3.1.38 or EC 1.3.1.44, such as, for example, the gene product of ter from Escherichia coli, Fibrobacter succinogenes, or Treponema denticola (Nishimaki et al., J. Biochem., 1984, 95:1315-1321; Shen et al., 2011, supra) or tdter from Treponema denticola (Bond-Watts et al., Biochemistry, 2012, 51:6827-6837) or EC 1.3.1.8 (Inui et al, Eur. J. Biochem., 1984, 142, 121-126).

In some embodiments, a polypeptide having the activity of a thioesterase may be classified under EC 3.1.2.-, such as, for example, the gene product of BT_2075 from Bacteroides thetaiotaomicron (strain ATCC 29148/DSM 2079/NCTC 10582/E50/VPI-5482) (GenBank Accession No. AAO77182.1, SEQ ID NO: 20), the gene product of lp_0708 from Lactobacillus plantarum (strain ATCC BAA-793/NCIMB 8826/WCFS1) (GenBank Accession No. CCC78182.1, SEQ ID NO: 22), the gene product of HMPREF0077_1317 from Anaerococcus tetradius ATCC 35098 (GenBank Accession No. EE182564.1, SEQ ID NO: 23), or the gene product of CPF_2954 from Clostridium perfringens (strain ATCC 13124/DSM 756/JCM 1290/NCIMB 6125/NCTC 8237/Type A) (GenBank Accession No. ABG82470.1, SEQ ID NO: 18).

In some embodiments, a polypeptide having the activity of a monooxygenase may be classified in the cytochrome P450 family under EC 1.14.14.- or EC 1.14.15.-, such as EC 1.14.14.1, EC 1.14.14.3, EC 1.14.15.1, or EC 1.14.15.3 or as the gene products of alkBGT from Pseudomonas putida, CYP153A from Polaromonas sp., or CYP52A3 from Saccharomyces cerevisiae.

In some embodiments, a polypeptide having the activity of an alcohol dehydrogenase may be classified under EC 1.1.1., such as a 6-hydroxyhexanoate dehydrogenase classified, for example, under EC 1.1.1.258, such as, for example, the gene product of chnD from Acinetobacter sp. NCIMB9871 (Donoghue et al., Eur. J. Biochem, 1975, 60: 1-7); or a 4-hydroxybutanoate dehydrogenase classified, for example, under EC 1.1.1.61 such as, for example, the gene product of gbd (e.g., from Sorangium cellulosum) or gabD from, for example, Escherichia coli (Bartsch et al., J. Bacteriol., 1990, 172(12), 7035). In some embodiments, a polypeptide having the activity of an aldehyde dehydrogenase may be classified under, for example, EC 1.2.1.-, such as a 7-oxoheptanoate dehydrogenase (e.g., the gene product of thnG from Sphingomonas macrogolitabida), a 6-oxohexanoate dehydrogenase (e.g., the gene product of chnE from Acinetobacter sp.) classified, for example, under EC 1.2.1.63, a 5-oxopentanoate dehydrogenase classified, for example, under EC 1.2.1.20 (e.g., the gene product of cpnE Comamonas sp.), a succinate-semialdehyde dehydrogenase classified, for example, under EC 1.2.1.16, EC 1.2.1.24, or EC 1.2.1.79 (e.g., the gene product of ALDH5F1 from Arabidopsis thaliana (UniProtKB Accession No. Q9SAK4), the gene product of araE from Azospirillum brasilense (UniProtKB Accession No. Q1JUP4), the gene product of Ssadh from Drosophila melanogaster (UniProtKB Accession No. Q9VBP6), the gene product of ALDH5A1 from Gorilla gorilla (UniProtKB Accession No. Q6A2H1), the gene product of ALDH5A1 from Hylobates lar (UniProtKB Accession No. Q3MSM3), the gene product of ssadh from Lucilia cuprina (UniProtKB Accession No. B0JFD4), the gene product of ALDH5A1 from Pan paniscus (UniProtKB Accession No. Q3MSM4), the gene product of ALDH5A1 from Pan troglodytes (UniProtKB Accession No. Q6A2H0), the gene product of ALDH5A1 from Pongo abelii (UniProtKB Accession No. Q6A2H2), the gene product of ALDH5A1 from Pongo pygmaeus (UniProtKB Accession No. Q6A2H2), or the gene product of gapN-1 from Sulfolobus solfataricus (UniProtKB Accession No. Q97XS9)), or an aldehyde dehydrogenase classified under EC 1.2.1.3.

As shown in FIG. 1 and FIG. 2, 9-oxononanoate may be converted to azelaic acid as by one or more exogenous polypeptides having the following enzymatic activities; for example, a 7-oxoheptanoate dehydrogenase (e.g., the gene product of thnG from Sphingomonas macrogolitabida) classified under EC 1.2.1.-, a 6-oxohextanoate dehydrogenase (e.g., the gene product of chnE from Acinetobacter sp.) classified, for example, under EC 1.2.1.63, a 5-oxopentanoate dehydrogenase classified, for example, under EC 1.2.1.20 (the gene product of cpnE from Comamonas sp.), a succinate-semialdehyde dehydrogenase classified, for example, under EC 1.2.1.16, EC 1.2.1.24, or EC 1.2.1.79, and/or an aldehyde dehydrogenase classified under EC 1.2.1.3.

As shown in FIG. 1 and FIG. 2, azelaic acid may be converted to pimeloyl-CoA by one or more exogenous polypeptides having the enzymatic activities of: a CoA ligase, an acyl-CoA dehydrogenase, an enoyl-CoA hydratase, a 3-hydroxyacyl-CoA dehydrogenase, a 3-oxoacyl-ACP reductase, and/or a β-ketothiolase. In some embodiments, a polypeptide having the activity of a CoA ligase may be classified under, for example, EC 6.2.1.-.

In some embodiments, a polypeptide having the activity of an acyl-CoA dehydrogenase may be classified under, for example, EC 1.3.8.-, such as EC 1.3.8.6, EC 1.3.8.7, or EC 1.3.8.8.

In some embodiments, a polypeptide having the activity of an enoyl-CoA hydratase may be classified under, for example, EC 4.2.1.17, such as, for example, the gene product of crt from Clostridium acetobutylicum, or classified under EC 4.2.1.119, such as, for example, the gene product of phaJ from Pseudomonas aeruginosa. In some embodiments, a polypeptide having the activity of a 3-hydroxyacyl-CoA dehydrogenase may be classified for example, under EC 1.1.1.-, such as EC 1.1.1.35 (e.g., the gene product of fadB from Escherichia coli), EC 1.1.1.36 (e.g., the gene product of phaB from Cupriavidus necator), or EC 1.1.1.157 (e.g., the gene product of hbd from Clostridium acetobutylicum), and a polypeptide having the activity of a 3-oxoacyl-ACP reductase may be classified, for example, under EC 1.1.1.100, such as, for example, the gene product of fabG from Escherichia coli.

In some embodiments, a polypeptide having the activity of a β-ketothiolase may be classified, for example, under EC 2.3.1.16 or EC 2.3.1.174 such as, for example, the gene product of bktB from Cupriavidus necator or paaJ from Escherichia coli.

Enzymes Generating the Terminal Carboxyl Groups in the Biosynthesis of Pimelic Acid

As depicted in FIG. 3, pimeloyl-CoA can be enzymatically converted to pimelic acid. The terminal carboxyl group leading to the production of pimelic acid can be enzymatically formed using polypeptides having the activity of a thioesterase, a CoA ligase, a CoA transferase, an aldehyde dehydrogenase, a succinate-semialdehyde dehydrogenase, a 5-oxopentanoate dehydrogenase, a 6-oxohexanoate dehydrogenase, and/or a 7-oxoheptanoate dehydrogenase.

In some embodiments, the second terminal carboxyl group leading to the synthesis of pimelic acid can be enzymatically formed in pimeloyl-CoA by a polypeptide having the activity of a thioesterase classified under EC 3.1.2.-. The polypeptide having the activity of a thioesterase can be, for example, the gene product of yciA from Escherichia coli or acot13 from Mus musculus (Cantu et al., Protein Science, 2010, 19, 1281-1295; Zhuang et al., Biochemistry, 2008, 47(9):2789-2796; Naggert et al., J. Biol. Chem., 1991, 266(17): 11044-11050), or tesB from Escherichia coli, or the gene product of BT_2075 from Bacteroides thetaiotaomicron (strain ATCC 29148/DSM 2079/NCTC 10582/E50/VPI-5482) (GenBank Accession No. AAO77182.1, SEQ ID NO: 20), the gene product of lp_0708 from Lactobacillus plantarum (strain ATCC BAA-793/NCIMB 8826/WCFS1) (GenBank Accession No. CCC78182.1, SEQ ID NO: 22), the gene product of HMPREF0077_1317 from Anaerococcus tetradius ATCC 35098 (GenBank Accession No. EE182564.1, SEQ ID NO: 23), or the gene product of CPF_2954 from Clostridium perfringens (strain ATCC 13124/DSM 756/JCM 1290/NCIMB 6125/NCTC 8237/Type A) (GenBank Accession No. ABG82470.1, SEQ ID NO: 18)).

In some embodiments, the second terminal carboxyl group leading to the synthesis of pimelic acid can be enzymatically formed in pimeloyl-CoA by a polypeptide having the activity of a CoA ligase classified under EC 6.2.1.-, such as EC 6.2.1.5 or EC 6.2.1.15, or a polypeptide having the activity of a CoA transferase classified under EC 2.8.3.-, such as EC 2.8.3.8 or EC 2.8.3.12 (e.g., a succinyl-CoA:acetate CoA-transferase from Acetobacter aceti (UniProtKB Accession No. B3EY95), the gene product of ANACAC_01149 from Anaerostipes caccae (UniProtKB Accession No. B0MC58), a butyryl-CoA:acetate CoA-transferase from Butyrivibrio fibrisolvens (UniProtKB Accession No. D2WEY7), a butyryl-CoA:acetate CoA-transferase from Eubacterium hallii (UniProtKB Accession No. D2WEY8), the gene product of FAEPRAA2165_01575 from Faecalibacterium prausnitzii (UniProtKB Accession No. C7H5K4), a butyryl-CoA:acetate CoA-transferase from Faecalibacterium prausnitzii (UniProtKB Accession No. D2WEZ2), the gene product of FAEPRAM212_02812 from Faecalibacterium prausnitzii (UniProtKB Accession No. A8SFP6), a butyryl-CoA transferase from Roseburia hominis (UniProtKB Accession No. Q2TME9), or a butyryl-CoA:acetate CoA-transferase from Roseburia inulinivorans (UniProtKB Accession No. D2WEY6)).

In some embodiments, pimeloyl-CoA can be enzymatically converted to pimelate semialdehyde by a polypeptide having the activity of an aldehyde dehydrogenase classified under, for example, EC 1.2.1.10, such as an acetaldehyde dehydrogenase encoded by pduB from Salmonella typhimurium. The second terminal carboxyl group leading to the synthesis of pimelic acid can be enzymatically formed in pimelate semialdehyde by a polypeptide having the activity of an aldehyde dehydrogenase classified under EC 1.2.1.3 (Guerrillot & Vandecasteele, Eur. J. Biochem., 1977, 81, 185-192); a 7-oxoheptanoate dehydrogenase (e.g., the gene product of thnG from Sphingomonas macrogolitabida; López-Sánchez et al., Appl. Environ. Microbiol., 2010, 76(1), 110-118) classified under EC 1.2.1.-; a 6-oxohextanoate dehydrogenase (e.g., the gene product of chnE from Acinetobacter sp.) classified, for example, under EC 1.2.1.63; a 5-oxopentanoate dehydrogenase classified, for example, under EC 1.2.1.20 (e.g., the gene product of cpnE from Comamonas sp.) or a succinate-semialdehyde dehydrogenase classified, for example, under EC 1.2.1.16, EC 1.2.1.24, or EC 1.2.1.79 (e.g., the gene product of ALDH5F1 from Arabidopsis thaliana (UniProtKB Accession No. Q9SAK4), the gene product of araE from Azospirillum brasilense (UniProtKB Accession No. Q1JUP4), the gene product of Ssadh from Drosophila melanogaster (UniProtKB Accession No. Q9VBP6), the gene product of ALDH5A1 from Gorilla gorilla (UniProtKB Accession No. Q6A2H1), the gene product of ALDH5A1 from Hylobates lar (UniProtKB Accession No. Q3MSM3), the gene product of ssadh from Lucilia cuprina (UniProtKB Accession No. B0JFD4), the gene product of ALDH5A1 from Pan paniscus (UniProtKB Accession No. Q3MSM4), the gene product of ALDH5A1 from Pan troglodytes (UniProtKB Accession No. Q6A2H0), the gene product of ALDH5A1 from Pongo abelii (UniProtKB Accession No. Q6A2H2), the gene product of ALDH5A1 from Pongo pygmaeus (UniProtKB Accession No. Q6A2H2), or the gene product of gapN-1 from Sulfolobus solfataricus (UniProtKB Accession No. Q97XS9)).

Enzymes Generating 7-Aminoheptanoate

As depicted in FIG. 4, pimeloyl-CoA is converted to pimelate semialdehyde by a polypeptide having the enzymatic activity of an aldehyde dehydrogenase classified under, for example, EC 1.2.1.10, such as an acetaldehyde dehydrogenase encoded by pduB from Salmonella typhimurium or pduP from Klebsiella pneumoniae. A terminal amine group may then be enzymatically formed or removed using one or more polypeptides having the activity of a ω-transaminase classified under, for example, EC 2.6.1.-, e.g., EC 2.6.1.18, EC 2.6.1.19, EC 2.6.1.29, EC 2.6.1.48, or EC 2.6.1.82, such as, for example, that obtained from Chromobacterium violaceum (GenBank Accession No. AAQ59697.1, SEQ ID NO: 7), Pseudomonas aeruginosa (GenBank Accession No. AAG08191.1, SEQ ID NO: 8), Pseudomonas syringae (GenBank Accession No. AAY39893.1, SEQ ID NO: 9), Rhodobacter sphaeroides (GenBank Accession No. ABA81135.1, SEQ ID NO: 10), Escherichia coli (GenBank Accession No. AAA57874.1, SEQ ID NO: 11, SEQ ID NO: 48), Vibrio fluvialis (GenBank Accession No. AEA39183.1, SEQ ID NO: 12), Streptomyces griseus, or Clostridium viride. See FIG. 8. The reversible ω-transaminase from Chromobacterium violaceum (GenBank Accession No. AAQ59697.1, SEQ ID NO: 7) has demonstrated analogous activity accepting 7-aminoheptanoic acid as amino donor, thus forming the first terminal amine group in pimelate semialdehyde (Kaulmann et al., Enzyme and Microbial Technology, 2007, 41, 628-637).

Alternatively, pimelate (pimelic acid) as shown in FIG. 3, may be enzymatically converted to pimelate semialdehyde by a polypeptide having the activity of a carboxylate reductase classified, for example, under EC 1.2.99.6 such as polypeptides represented by the following GenBank Accession Nos: EFV11917.1 (SEQ ID NO: 3) and ADG98140.1 (SEQ ID NO: 6). A terminal amine group may then be enzymatically formed or removed from pimelate semialdehyde using one or more polypeptides having the activity of a ω-transaminase classified under, for example, EC 2.6.1.-, e.g., EC 2.6.1.18, EC 2.6.1.19, EC 2.6.1.29, EC 2.6.1.48, or EC 2.6.1.82, such as, for example, that obtained from Chromobacterium violaceum (GenBank Accession No. AAQ59697.1, SEQ ID NO: 7), Pseudomonas aeruginosa (GenBank Accession No. AAG08191.1, SEQ ID NO: 8), Pseudomonas syringae (GenBank Accession No. AAY39893.1, SEQ ID NO: 9), a Rhodobacter sphaeroides (GenBank Accession No. ABA81135.1, SEQ ID NO: 10), Vibrio fluvialis (GenBank Accession No. AEA39183.1, SEQ ID NO: 12), Streptomyces griseus, or Clostridium viride. See FIG. 8. The reversible ω-transaminase from Chromobacterium violaceum (GenBank Accession No. AAQ59697.1, SEQ ID NO: 7) has demonstrated analogous activity accepting 7-aminoheptanoic acid as amino donor, 51 thus forming the first terminal amine group in pimelate semialdehyde (Kaulmann et al., Enzyme and Microbial Technology, 2007, 41, 628-637).

An additional ω-transaminase that can be used in the methods and microorganisms described herein is from Escherichia coli (GenBank Accession No. AAA57874.1, SEQ ID NO: 11, SEQ ID NO: 48). Some of the ω-transaminases classified, for example, under EC 2.6.1.29 or EC 2.6.1.82 are diamine ω-transaminases (e.g., SEQ ID NO: 11, SEQ ID NO: 48).

The reversible ω-transaminase from Chromobacterium violaceum (GenBank Accession No. AAQ59697.1, SEQ ID NO: 7) has demonstrated analogous activity accepting 7-aminoheptanoic acid as amino donor, thus forming the first terminal amine group in pimelate semialdehyde (Kaulmann et al., Enzyme and Microbial Technology, 2007, 41, 628-637).

Enzymes Generating the Terminal Amine Groups in the Biosynthesis of Heptamethylenediamine

As depicted in FIG. 5, terminal amine groups can be enzymatically formed or removed using polypeptides having the activity of a ω-transaminase or a deacylase.

In some embodiments, a terminal amine group leading to the synthesis of 7-aminoheptanoic acid is enzymatically formed in 7-aminoheptanal by a polypeptide having the activity of a ω-transaminase classified, for example, under EC 2.6.1.-, e.g., EC 2.6.1.18, EC 2.6.1.19, EC 2.6.1.29, EC 2.6.1.48, or EC 2.6.1.82, such as that obtained, for example, from Chromobacterium violaceum (GenBank Accession No. AAQ59697.1, SEQ ID NO: 7), Pseudomonas aeruginosa (GenBank Accession No. AAG08191.1, SEQ ID NO: 8), Pseudomonas syringae (GenBank Accession No. AAY39893.1, SEQ ID NO: 9), Rhodobacter sphaeroides (GenBank Accession No. ABA81135.1, SEQ ID NO: 10), Vibrio fluvialis (GenBank Accession No. AEA39183.1, SEQ ID NO: 12), Streptomyces griseus, or Clostridium viride. See FIG. 8.

An additional polypeptide having the activity of a ω-transaminase that can be used in the methods and microorganisms described herein is from Escherichia coli (GenBank Accession No. AAA57874.1, SEQ ID NO: 11, SEQ ID NO: 48). Some of the polypeptides having the activity of ω-transaminases classified, for example, under EC 2.6.1.29 or EC 2.6.1.82 are diamine ω-transaminases (e.g., SEQ ID NO: 11, SEQ ID NO: 48).

The reversible ω-transaminase from Chromobacterium violaceum (GenBank Accession No. AAQ59697.1, SEQ ID NO: 7) has demonstrated analogous activity accepting 7-aminoheptanoic acid as amino donor, thus forming the first terminal amine group in pimelate semialdehyde (Kaulmann et al., Enzyme and Microbial Technology, 2007, 41, 628-637).

The reversible 4-aminobubyrate:2-oxoadipate transaminase from Streptomyces griseus has demonstrated activity for the conversion of 7-aminoheptanoate to pimelate semialdehyde (Yonaha et al., Eur. J. Biochem., 1985, 146, 101-106).

The reversible 5-aminovalerate transaminase from Clostridium viride has demonstrated activity for the conversion of 7-aminoheptanoate to pimelate semialdehyde (Barker et al., J. Biol. Chem., 1987, 262(19), 8994-9003).

In some embodiments, the second terminal amine group leading to the synthesis of heptamethylenediamine is enzymatically formed in 7-aminoheptanal by a polypeptide having the activity of a diamine transaminase classified, for example, under EC 2.6.1.29 or classified, for example, under EC 2.6.1.82, such as, for example, the gene product of ygjG from E. coli (GenBank Accession No. AAA57874.1, SEQ ID NO: 11, SEQ ID NO: 48). The polypeptides having the activity of a transaminase set forth in SEQ ID NOs: 7-10 and 12 also can be used to produce heptamethylenediamine. See FIG. 8.

The gene product of ygjG from Escherichia coli accepts a broad range of diamine carbon chain length substrates, such as putrescine, cadaverine and spermidine (Samsonova et al, BMC Microbiology, 2003, 3:2).

The diamine transaminase from E. coli strain B has demonstrated activity for 1,7 diaminoheptane (Kim, The Journal of Chemistry, 1964, 239(3), 783-786).

In some embodiments, the second terminal amine group leading to the synthesis of heptamethylenediamine is enzymatically formed in N7-acetyl-1,7%-diaminoheptane by a polypeptide having the activity of a deacylase classified, for example, under EC 3.5.1.-, such as, for example, EC 3.5.1.62 or EC 3.5.1.82.

Enzymes Generating the Terminal Hydroxyl Groups in the Biosynthesis of 7-Hydroxyheptanoate

As depicted in FIG. 6, pimelic acid, as shown in FIG. 3, may be converted to pimelate semialdehyde by a polypeptide having the activity of a carboxylate reductase classified, for example, under EC 1.2.99.6, such as, for example, the polypeptides represented by the following GenBank Accession Numbers: EFV11917.1 (SEQ ID NO: 3) or ADG98140.1 (SEQ ID NO: 6). Having formed pimelate semialdehyde, a terminal hydroxyl group can then be enzymatically formed (or removed) using one or more polypeptides having the activity of an alcohol dehydrogenase classified, for example, under EC 1.1.1.-, such as, for example, a 5-hydroxypentanoate dehydrogenase, such as, for example, the gene product of cpnD from Comamonas sp (Iwaki et at, Appl. Environ. Microbiol., 1999, 65(11):5158-5162), or a 4-hydroxybutanoate dehydrogenase, such as, for example, the gene product of gabD from Escherichia coli (Bartsch et al., J. Bacteriol., 1990, 172(12), 7035). The polypeptide having the activity of an alcohol dehydrogenase may also be classified under EC 1.1.1.258, such as a 6-hydroxyhexanoate dehydrogenase, such as, for example, the gene product of chnD from Acinetobacter sp. NCIMB9871 (Donoghue et al., Eur. J. Biochem, 1975, 60: 1-7).

Alternatively, as shown in FIG. 6, pimeloyl-CoA may be converted to pimelate semialdehyde by an polypeptide having the activity of an alcohol dehydrogenase classified, for example, under EC 1.2.1.10, such as a polypeptide having the activity of an acetaldehyde dehydrogenase encoded by pduB from Salmonella typhimurium or pduP from Klebsiella pneumoniae. Having formed pimelate semialdehyde, a terminal hydroxyl group can then be enzymatically formed (or removed) using one or more polypeptides having the activity of an alcohol dehydrogenase classified, for example, under EC 1.1.1.- such as a 5-hydroxypentanoate dehydrogenase, such as, for example, the gene product of cpnD from Comamonas sp. (Iwaki et al., Appl. Environ. Microbial., 1999, 65(11):5158-5162), or a 4-hydroxybutanoate dehydrogenase, such as, for example, the gene product of gabD from Escherichia coli (Bartsch et al., J. Bacteriol., 1990, 172(12), 7035). The polypeptide having the activity of an alcohol dehydrogenase may also be classified under EC 1.1.1.258, such as a 6-hydroxyhexanoate dehydrogenase, such as, for example, the gene product of chnD from Acinetobacter sp. NCIMB9871 (Donoghue et al., Eur. J. Biochem, 1975, 60: 1-7).

Enzymes Generating the Terminal Hydroxyl Groups in the Biosynthesis of 1,7 Heptanediol

As depicted in FIG. 7, the terminal hydroxyl group can be enzymatically formed using a polypeptide having the activity of an alcohol dehydrogenase. For example, the second terminal hydroxyl group leading to the synthesis of 1,7 heptanediol can be enzymatically formed in 7-hydroxyheptanal by a polypeptide having the activity of an alcohol dehydrogenase classified under EC 1.1.1.- (e.g., EC 1.1.1.1, EC 1.1.1.2, EC 1.1.1.21, or EC 1.1.1.184), such as, for example, the gene product of YMR318C from Saccharomyces cerevisiae or yqhD from Escherichia coli (Liu et al., Microbiology, 2009, 155, 2078-2085; Larroy et al., 2002, Biochem J., 361(Pt 1), 163-172; Jarboe, 2011, Appl. Microbiol. Biotechnol., 89(2), 249-257) or the polypeptide represented by GenBank Accession No. CAA81612.1 (SEQ ID NO: 21). The alcohol dehydrogenase encoded by YMR318C has broad substrate specificity, including the oxidation of C7 alcohols. The polypeptide having the activity of an alcohol dehydrogenase classified under EC 1.1.1.- may also be a polypeptide represented by GenBank Accession CAA81612.1 (SEQ ID NO: 21).

Biochemical Pathways Pathways to Pimeloyl-CoA

In some embodiments, and as shown in FIG. 1 and FIG. 2, the central metabolite octadecanoyl-CoA is converted to octadec-9-enoyl-CoA using a polypeptide having the enzymatic activity of a delta9-desaturase classified under, for example, EC 1.14.19.1; followed by conversion of octadec-9-enoyl-CoA to octadec-9,12-dienoyl-CoA using a polypeptide having the enzymatic activity of a delta12-desaturase classified under, for example, EC 1.14.19.6; followed by conversion of octadec-9,12-dienoyl-CoA to linoleic acid using a polypeptide having the enzymatic activity of a thioesterase classified under, for example, EC 3.1.2-; followed by conversion of linoleic acid using a polypeptide having the enzymatic activity of a 9-lipoxygenase classified under, for example, EC 1.13.11.58, EC 1.13.11.60, EC 1.13.11.61, or EC 1.13.11.62.

In some embodiments, and as shown in FIG. 1 and FIG. 2, 9-hydroxyperoxyoctadec-10,12-dienoate is cleaved by a polypeptide having the enzymatic activity of a hydroperoxide lyase classified, for example, under EC 4.2.99.-, such as, for example, a polypeptide represented by GenBank Accession No. AAF64041.1 (SEQ ID NO: 13) or a polypeptide represented by GenBank Accession No. BAG97978.1 (SEQ ID NO: 14), to produce non-3-enal and 9-oxononanoate.

In some embodiments, and as shown in FIG. 1, non-3-enal is converted to non-3-2a enoate by one or more polypeptides having the enzymatic activity of an aldehyde dehydrogenase classified, for example, under EC 1.2.1.-. such as EC 1.2.1.3, EC 1.2.1.4, EC 1.2.1.5, or EC 1.2.1.48, such as, for example, the gene product of Bt-aldh from Geobacillus thermoleovorans 23 (UniProtKB Accession No. Q9FAB1), the gene product of dhaS from Bacillus subtilis (UniProtKB Accession No. O34660), the gene 2 product of ALD5 from Saccharomyces cerevisiae (UniProtKB Accession No. A6ZR27), the gene product of ALDH2C4 from Arabidopsis thaliana (UniProtKB Accession No. Q56YU0), the gene product of aldh7 from Rhodococcus ruber (UniProtKB Accession No. Q840S9), the gene product of alkH from Pseudomonas oleovorans (UniProtKB Accession No. P12693), the gene product of ald1 from Acinetobacter sp. M-1 (UniProtKB Accession No. Q9FDS1), or the gene product of acoD from Ralstonia eutropha (UniProtKB Accession No. P46368); followed by conversion of non-3-enoate to non-3-enoyl-CoA by a polypeptide having the enzymatic activity of a CoA ligase classified, for example, under EC 6.2.1.-, such as, for example, the gene product of acs6 from Brassica napus (UniProtKB Accession No. Q9FNT6), the gene product of PCS60 from Saccharomyces cerevisiae (UniProtKB Accession No. P38137), the gene product of alkK from Pseudomonas oleovorans (UniProtKB Accession No. Q00594), the gene product of ACSM5 from Homo sapiens (UniProtKB Accession No. Q6NUN0), or the gene product of alkK from Aeropyrum pernix (UniProtKB Accession No. Q9YF45); followed by conversion of non-3-enoyl-CoA to non-2-enoyl-CoA by a polypeptide having the enzymatic activity of a dodecenoyl-CoA isomerase classified, for example, under EC 5.3.3.8; followed by conversion of non-2-enoyl-CoA to nonanoyl-CoA by a trans-2-enoyl-CoA reductase classified, for example, under EC 1.3.1.38, EC 1.3.1.44 such as, for example, the gene product of ter from Escherichia coli, Fibrobacter succinogenes, or Treponema denticola (Nishimaki et al, J. Biochem., 1984, 95:1315-1321; Shen et al, 2011, supra) or tdter from Treponema denticola (Bond-Watts et al., Biochemistry, 2012, 51:6827-6837) or EC 1.3.1.8 (Inui et al, Eur. J. Biochem., 1984, 142, 121-126); followed by conversion of nonanoyl-CoA to nonanoic acid using a polypeptide having the enzymatic activity of a thioesterase classified, for example, under EC 3.1.2.-, such as, for example, the gene product of BT_2075 from Bacteroides thetaiotaomicron (strain ATCC 29148/DSM 2079/NCTC 10582/E50/VPI-5482) (GenBank Accession No. AAO77182.1, SEQ ID NO: 20), the gene product of lp_0708 from Lactobacillus plantarum (strain ATCC BAA-793/NCIMB 8826/WCFS1) (GenBank Accession No, CCC78182.1, SEQ ID NO: 22), the gene product of HMPREF0077_1317 from Anaerococcus tetradius ATCC 35098 (GenBank Accession No. EEI82564.1, SEQ ID NO: 23), or the gene product of CPF_2954 from Clostridium perfringens (strain ATCC 13124/DSM 756/JCM 1290/NCIMB 6125/NCTC 8237/Type A) (GenBank Accession No. ABG82470.1), SEQ ID NO: 18); followed by conversion of nonanoic acid to 9-hydroxynonanoic acid using a polypeptide having the enzymatic activity of a monooxygenase classified, for example, under EC 1.14.14- or EC 1.14.15.-, such as EC 1.14.14.1, EC 1.14.14.3, EC 1.14.15.1 or EC 1.14.15.3 and as encoded by alkBGT from Pseudomonas putida, CYP153A from Polaromonas sp., or CYP52A3 from Saccharomyces cerevisiae; followed by conversion of 9-hydroxynonanoic acid to 9-oxononanoate using a polypeptide having the enzymatic activity of an alcohol dehydrogenase classified under EC 1.1.1.-, a 6-hydroxyhexanoate dehydrogenase classified under EC 1.1.1.258, such as, for example, the gene product of chnD from Acinetobacter sp. NCIMB9871 (Donoghue et al., Eur. J. Biochem, 1975, 60: 1-7); or a 4-hydroxybutanoate dehydrogenase classified under EC 1.1.1.61, such as, for example, the gene product of gabD from Escherichia coli (Bartsch et al., J. Bacteriol., 1990, 172(12), 7035); followed by conversion of 9-oxononanoate to azelaic acid using a polypeptide having the enzymatic activity of an aldehyde dehydrogenase classified under, for example, EC 1.2.1.- such as a 7-oxoheptanoate dehydrogenase (e.g., the gene product of thnG from Sphingomonas macrogolitabida), a 6-oxohextanoate dehydrogenase (e.g., the gene product of chnE from Acinetobacter sp.) classified, for example, under EC 1.2.1.63, a 5-oxopentanoate dehydrogenase classified, for example, under EC 1.2.1.20 (e.g., the gene product of cpnE from Comamonas sp.), a succinate-semialdehyde dehydrogenase classified, for example, under EC 1.2.1.16, EC 1.2.1.24, or EC 1.2.1.79, or an aldehyde dehydrogenase classified under EC 1.2.1.3.

In some embodiments, and as shown in FIG. 2, non-3-enal is converted to non-2-enal by a polypeptide having the enzymatic activity of an enal isomerase classified, for example, under EC 5.3.3.-; followed by conversion of non-2-al to nonanal by a polypeptide having the enzymatic activity of an enoate reductase classified, for example, under EC 1.3.1.31; followed by conversion of nonanal to nonanoic acid by a polypeptide having the enzymatic activity of an aldehyde dehydrogenase classified, for example, under EC 1.2.1.-. such as EC 1.2.1.3, EC 1.2.1.4, EC 1.2.1.5, or EC 1.2.1.48, such as, for example, the gene product of Bt-aldh from Geobacillus thermoleovorans B23 (UniProtKB Accession No. Q9FAB1), the gene product of dhaS from Bacillus subtilis (UniProtKB Accession No. O34660), the gene product of ALD5 from Saccharomyces cerevisiae (UniProtKB Accession No. A6ZR27), the gene product of ALDH2C4 from Arabidopsis thaliana (UniProtKB Accession No. Q56YU0), the gene product of aldh7 from Rhodococcus ruber (UniProtKB Accession No. Q840S9), the gene product of alkH from Pseudomonas oleovorans (UniProtKB Accession No. P12693), the gene product of ald1 from Acinetobacter sp. Ma-1 (UniProtKB Accession No. Q9FDS1), or the gene product of acoD from Ralstonia eutropha (UniProtKB Accession No. P46368); followed by conversion of nonanoic acid to 9-hydroxynonanoic acid by a monooxygenase classified, for example, under EC 1.14.14- or EC 1.14.15.-, such as EC 1.14.14.1, EC 1.14.14.3, EC 1.14.15.1, or EC 1.14.15.3 or encoded by alkBGT from Pseudomonas putida, CYP153A from Polaromonas sp., or CYP52A3 from Saccharomyces cerevisiae; followed by conversion of 9-hydroxynonanoic acid to 9-oxononanoic acid by a polypeptide having the enzymatic activity of an alcohol dehydrogenase classified under EC 1.1.1.-, a 6-hydroxyhexanoate dehydrogenase classified under EC 1.1.1.258, such as, for example, the gene product of chnD from Acinetobacter sp. NCIMB9871 (Donoghue et al., Eur. J. Biochem, 1975, 60: 1-7); or a 4-hydroxybutanoate dehydrogenase classified under EC 1.1.1.61, such as, for example, the gene product of gabD from Escherichia coli (Bartsch et al, J. Bacteriol., 1990, 172(12), 7035); followed by conversion of 9-oxononanoate to azelaic acid using a polypeptide having the enzymatic activity of an aldehyde dehydrogenase classified under, for example, EC 1.2.1.-, such as a 7-oxoheptanoate dehydrogenase (e.g., the gene product of thnG from Sphingomonas macrogolitabida), a 6-oxohextanoate dehydrogenase (e.g., the gene product of chnE from Acinetobacter sp.) classified, for example, under EC 1.2.1.63, a 5-oxopentanoate dehydrogenase classified, for example, under EC 1.2.1.20 (e.g., the gene product of cpnE from Comamonas sp.), a succinate-semialdehyde dehydrogenase classified, for example, under EC 1.2.1.16, EC 1.2.1.24, or EC 1.2.1.79 (e.g., the gene product of ALDH5F1 from Arabidopsis thaliana (UniProtKB Accession No. Q9SAK4), the gene product of araE from Azospirillum brasilense (UniProtKB Accession No. Q1JUP4), the gene product of Ssadh from Drosophila melanogaster (UniProtKB Accession No. Q9VBP6), the gene product of ALDH5A1 from Gorilla gorilla (UniProtKB Accession No. Q6A2H1), the gene product of ALDH5A1 from Hylobates lar (UniProtKB Accession No. Q3MSM3), the gene product of ssadh from Lucilia cuprina (UniProtKB Accession No. B0JFD4), the gene product of ALDH5A1 from Pan paniscus (UniProtKB Accession No. Q3MSM4), the gene product of ALDH5A1 from Pan troglodytes (UniProtKB Accession No. Q6A2H0), the gene product of ALDH5A1 from Pongo abelii (UniProtKB Accession No. Q6A2H2), the gene product of ALDH5A1 from Pongo pygmaeus (UniProtKB Accession No. Q6A2H2), or the gene product of gapN-1 from Sulfolobus solfataricus (UniProtKB Accession No. Q97XS9)), or an aldehyde dehydrogenase classified under EC 1.2.1.3.

In some embodiments, and as shown in FIGS. 1 and 2, 9-oxononanoate is converted to azelaic acid using a polypeptide having the activity of an aldehyde dehydrogenase classified under, for example, EC 1.2.1.-, such as a 7-oxoheptanoate dehydrogenase (e.g., the gene product of thnG from Sphingomonas macrogolitabida), a 6-oxohextanoate dehydrogenase (e.g., the gene product of chnE from Acinetobacter sp.) classified, for example, under EC 1.2.1.63, a 5-oxopentanoate dehydrogenase classified, for example, under EC 1.2.1.20 (e.g., the gene product of cpnE from Comamonas sp.), a succinate-semialdehyde delhydrogenase classified, for example, under EC 1.2.1.16, EC 1.2.1.24, or EC 1.2.1.79 (e.g., the gene product of ALDH5F1 from Arabidopsis thaliana (UniProtKB Accession No. Q9SAK4), the gene product of araE from Azospirillum brasilense (UniProtKB Accession No. Q1JUP4), the gene product of Ssadh from Drosophila melanogaster (UniProtKB Accession No. Q9VBP6), the gene product of ALDH5A1 from Gorilla gorilla (UniProtKB Accession No. Q6A2H1), the gene product of ALDH5A1 from Hylobates lar (UniProtKB Accession No. Q3MSM3), the gene product of ssadh from Lucilia cuprina (UniProtKB Accession No. B0JFD4), the gene so product of ALDH5A1 from Pan paniscus (UniProtKB Accession No. Q3MSM4), the gene product of ALDH5A1 from Pan troglodytes (UniProtKB Accession No. Q6A2H0), the gene product of ALDH5A1 from Pongo abelii (UniProtKB Accession No. Q6A2H2), the gene product of ALDH5A1 from Pongo pygmaeus (UniProtKB Accession No. Q6A2H2), or the gene product of gapN-1 from Sulfolobus solfataricus (UniProtKB a Accession No. Q97XS9)), or an aldehyde dehydrogenase classified under EC 1.2.1.3.

In some embodiments, and as shown in FIG. 1 and FIG. 2, azelaic acid is converted to azelaoyl-CoA by a polypeptide having the enzymatic activity of a CoA ligase classified, for example, under EC 6.2.1.-, such as, for example, the gene product of acs6 from Brassica napus (UniProtKB Accession No. Q9FNT6), the gene product of PCS60 from Saccharomyces cerevisiae (UniProtKB Accession No. P38137), the gene product of alkK from Pseudomonas oleovorans (UniProtKB Accession No. Q00594), the gene product of ACSM5 from Homo sapiens (UniProtKB Accession No. Q6NUN0), or the gene product of alkK from Aeropyrum pernix (UniProtKB Accession No. Q9YF45); followed by conversion of azelaoyl-CoA to 2,3-dehydro-azelaoyl-CoA using a polypeptide having the enzymatic activity of an acyl-CoA dehydrogenase classified, for example, under EC 1.3.8.-, such as EC 1.3.8.6, EC 1.3.8.7 or EC 1.3.8.8; followed by conversion of 2,3-dehydro-azelaoyl-CoA to 3-hydroxy-azelaoyl-CoA by a polypeptide having the enzymatic activity of an enoyl-CoA hydratase classified, for example, under EC 4.2.1.17, such as, for example, the gene product of crt from Clostridium acetobutylicum, or classified under EC 4.2.1.119, such as, for example, the gene product of phaJ from Pseudomonas aeruginosa; followed by conversion of 3-hydroxy-azelaoyl-CoA to 3-oxo-azelaoyl-CoA by a polypeptide having the enzymatic activity of a 3-hydroxyacyl-CoA dehydrogenase classified for example, under EC 1.1.1.-, such as EC 1.1.1.35 (e.g., the gene product of fadB from Escherichia coli), EC 1.1.1.36 (e.g., the gene product of phaB from Cupriavidus necator), or EC 1.1.1.157 (e.g., the gene product of hbd from Clostridium acetobutylicum) or a 3-oxoacyl-ACP reductase classified, for example, under EC 1.1.1.100, such as, for example, the gene product of fabG from Escherichia coli; followed by conversion of 3-oxo-azelaoyl-CoA to pimeloyl-CoA by a polypeptide having the enzymatic activity of a β-ketothiolase classified, for example, 2 under EC 2.3.1.16 or EC 2.3.1.174 such as, for example, the gene product of bktB from Cupriavidus necator or paaJ from Escherichia coli.

Pathways Using Pimeloyl-CoA as Central Precursor to Pimelic Acid

In some embodiments, pimelic acid is synthesized from pimeloyl-CoA by a polypeptide having the activity of a thioesterase classified under, for example, EC 3.1.2.-. The polypeptide having the activity of a thioesterase can be the gene product of yciA from Escherichia coli or acot13 from Mus musculus (Cantu et al., Protein Science, 2010, 19, 1281-1295; Zhuang et al., Biochemistry, 2008, 47(9):2789-2796; Naggert et al., J. Biol. Chem., 1991, 266(17):11044-11050), or tesB from Escherichia coli or a polypeptide represented by one of the following GenBank accession numbers: AAO77182.1 (SEQ ID NO: 20); CCC78182.1 (SEQ ID NO: 22); EE182564.1 (SEQ ID NO: 23); or ABG82470.1 (SEQ ID NO: 18).

In some embodiments, pimelic acid is synthesized from pimeloyl-CoA by a polypeptide having the activity of a CoA ligase classified under, for example, EC 6.2.1.-, such as EC 6.2.1.5 or EC 6.2.1.15, or a CoA transferase classified under, for example, EC 2.8.3.-, such as EC 2.8.3.8 or EC 2.8.3.12 (e.g., a succinyl-CoA:acetate CoA-transferase from Acetobacter aceti (UniProtKB Accession No. B3EY95), the gene product of ANACAC_01149 from Anaerostipes caccae (UniProtKB Accession No. B0MC58), a butyryl-CoA:acetate CoA-transferase from Butyrivibrio fibrisolvens (UniProtKB Accession No. D2WEY7), a butyryl-CoA:acetate CoA-transferase from Eubacterium hallii (UniProtKB Accession No. D2WEY8), the gene product of FAEPRAA2165_01575 from Faecalibacterium prausnitzii (UniProtKB Accession No. C7H5K4), a butyryl-CoA:acetate CoA-transferase from Faecalibacterium prausnitzii (UniProtKB Accession No. D2WEZ2), the gene product of FAEPRAM212.02812 from Faecalibacterium prausnitzii (UniProtKB Accession No. A8SFP6), a butyryl-CoA transferase from Roseburia hominis (UniProtKB Accession No. Q2TME9), or a butyryl-CoA:acetate CoA-transferase from Roseburia inulinivorans (UniProtKB Accession No. D2WEY6)).

In some embodiments, pimeloyl-CoA is converted to pimelate semialdehyde by a polypeptide having the activity of an aldehyde dehydrogenase, such as an acetaldehyde dehydrogenase classified under, for example, EC 1.2.1.10, such as that encoded by pduB from Salmonella typhimurium.

Pimelate semialdehyde is then converted to pimelic acid by a polypeptide having the activity of an aldehyde dehydrogenase classified under, for example, EC 1.2.1.-, such as a 7-oxoheptanoate dehydrogenase (e.g., the gene product of thnG from Sphingomonas macrogolitabida), a 6-oxohextanoate dehydrogenase (e.g., the gene product of chnE from Acinetobacter sp.) classified, for example, under EC 1.2.1.63, a 5-oxopentanoate dehydrogenase classified, for example, under EC 1.2.1.20 (e.g., the gene product of cpnE from Comamonas sp.), a succinate-semialdehyde dehydrogenase classified, for example, under EC 1.2.1.16, EC 1.2.1.24, or EC 1.2.1.79, or an aldehyde dehydrogenase classified under EC 1.2.1.3. See FIG. 3.

Pathways Using Pimeloyl-CoA as Central Precursor to 7-Aminoheptanoate

In some embodiments, pimeloyl-CoA is converted to pimelate semialdehyde using a polypeptide having the enzymatic activity of an aldehyde dehydrogenase classified under, for example, EC 1.2.1.10, such as an acetaldehyde dehydrogenase encoded by pduB from Salmonella typhimurium or pduP from Klebsiella pneumoniae. Pimelate semialdehyde is then converted to 7-aminoheptanoate using a polypeptide having the enzymatic activity of a ω-transaminase classified, for example, under EC 2.6.1.-, e.g., EC 2.6.1.18, EC 2.6.1.19, EC 2.6.1.29, EC 2.6.1.48, or EC 2.6.1.82, such as, for example, that obtained from Chromobacterium violaceum (GenBank Accession No. AAQ59697.1, SEQ ID NO: 7), Pseudomonas aeruginosa (GenBank Accession No. AAG08191.1, SEQ ID NO: 8), Pseudomonas syringae (GenBank Accession No. AAY39893.1, SEQ ID NO: 9), Rhodobacter sphaeroides (GenBank Accession No. ABA81135.1, SEQ ID NO: 10), Vibrio fluvialis (GenBank Accession No. AEA39183.1, SEQ ID NO: 12), Streptomyces griseus, or Clostridium viride.

In some embodiments, pimelate (see FIG. 3) is converted to pimelate semialdehyde using a polypeptide having the enzymatic activity of a carboxylate reductase classified, for example, under EC 1.2.99.6 such as, for example, the gene product of car in combination with a phosphopantetheine transferase enhancer (e.g., encoded by a sfp gene from Bacillus subtilis or npt gene from Nocardia) or the gene products of griC and griD from Streptomyces griseus (Suzuki et al., J. Antibiot., 2007, 60(6), 380-387). The polypeptide having the activity of a carboxylate reductase can be obtained, for example, from Mycobacterium marinum (GenBank Accession No. ACC40567.1, SEQ ID NO: 1), Mycobacterium smegmatis (GenBank Accession No. ABK71854.1, SEQ ID NO: 2), Segniliparus rugosus (GenBank Accession No. EFV11917.1, SEQ ID NO: 3), Mycobacterium smegmatis (GenBank Accession No. ABK75684.1, SEQ ID NO: 4), Mycobacterium massiliense (GenBank Accession No. EIV11143.1, SEQ ID NO: 5), or Segniliparus rotundus (GenBank Accession No. ADG98140.1, SEQ ID NO: 6). Pimelate semialdehyde is then converted to 7-aminoheptanoate using a polypeptide having the enzymatic activity of a ω-transaminase classified, for example, under EC 2.6.1.-, e.g., EC 2.6.1.18, EC 2.6.1.19, EC 2.6.1.29, EC 2.6.1.48, or EC 2.6.1.82, such as that obtained from Chromobacterium violaceum (GenBank Accession No. AAQ59697.1, SEQ ID NO: 7), Pseudomonas aeruginosa (GenBank Accession No. AAG08191.1, SEQ ID NO: 8), Pseudomonas syringae (GenBank Accession No. AAY39893.1, SEQ ID NO: 9), Rhodobacter sphaeroides (GenBank Accession No. ABA81135.1, SEQ ID NO: 10), Vibrio fluvialis (GenBank Accession No. AEA39183.1, SEQ ID NO: 12), Streptomyces griseus, or Clostridium viride. See FIG. 4.

Pathways Using Pimeloyl-CoA as Central Precursor to 7-Hydroxyheptanoate

In some embodiments, 7-hydroxyheptanoate is synthesized from the central precursor, pimeloyl-CoA using a polypeptide having the enzymatic activity of an aldehyde dehydrogenase classified under, for example, EC 1.2.1.10, such as an acetaldehyde dehydrogenase encoded by pduB from Salmonella typhimurium or pduP from Klebsiella pneumoniae; followed by conversion of pimelate semialdehyde to 7-hydroxyheptanoate by a polypeptide having the activity of an alcohol dehydrogenase classified, for example, under EC 1.1.1.2 such as, for example, the gene product of YMR318C from Saccharomyces cerevisiae, a 6-hydroxyhexanoate dehydrogenase classified, for example, under EC 1.1.1.258, a 5-hydroxypentanoate dehydrogenase classified, for example, under EC 1.1.1.-, such as, for example, the gene product of cpnD from Comamonas sp. (Iwaki et al., Appl. Environ. Microbiol., 1999, 65(11):5158-5162), or a 4-hydroxybutanoate dehydrogenase classified, for example, under EC 1.1.1.- such as, for example, the gene product of gabD from Escherichia coli (Bartsch et al., J. Bacteriol., 1990, 172(12), 7035). The alcohol dehydrogenase encoded by YMR318C has broad substrate specificity, including the oxidation of C7 alcohols. See FIG. 6.

Pathway Using 7-Aminoheptanoate, 7-Hydroxyheptanoate, Pimelate Semialdehyde, or as 1,7-Heptanediol as a Central Precursor to Heptamethylenediamine

In some embodiments, heptamethylenediamine is synthesized from the central precursor, 7-aminoheptanoate (which can be produced as described in FIG. 4), by conversion of 7-aminoheptanoate to 7-aminoheptanal by a polypeptide having the activity of a carboxylate reductase classified, for example, under EC 1.2.99.6, such as, for example, the gene product of car in combination with a phosphopantetheine transferase enhancer (e.g., encoded by a sfp gene from Bacillus subtilis or npt gene from Nocardia) or the gene products of griC and griD from Streptomyces griseus (Suzuki et al., J. Antibiot., 2007, 60(6), 380-387); followed by conversion of 7-aminoheptanal to heptamethylenediamine by a polypeptide having the activity of a ω-transaminase such as a ω-transaminase classified under EC 2.6.1.- (e.g., EC 2.6.1.18, EC 2.6.1.19, EC 2.6.1.48, or EC 2.6.1.82, such as, for example, SEQ ID NOs: 7-12). The polypeptide having the activity of a carboxylate reductase can be obtained, for example, from Mycobacterium marinum (GenBank Accession No. ACC40567.1, SEQ ID NO: 1), Mycobacterium smegmatis (GenBank Accession No. ABK71854.1, SEQ ID NO: 2), Segniliparus rugosus (GenBank Accession No. EFV11917.1, SEQ ID NO: 3), Mycobacterium smegmatis (GenBank Accession No. ABK75684.1, SEQ ID NO: 4), Mycobacterium massiliense (GenBank Accession No. EIV11143.1, SEQ ID NO: 5), or Segniliparus rotundus (GenBank Accession No. ADG98140.1, SEQ ID NO: 6).

The carboxylate reductase encoded by the gene product of car and enhancer npt from Nocardia or sfp from Bacillus subtilis has broad substrate specificity, including terminal difunctional C4 and C5 carboxylic acids (Venkitasubramanian et al., Enzyme and Microbial Technology, 2008, 42, 130-137).

In some embodiments, heptamethylenediamine is synthesized from the central precursor, 7-hydroxyheptanoate (which can be produced as described in FIG. 6), by conversion of 7-hydroxyheptanoate to 7-hydroxyheptanal by a polypeptide having the activity of a carboxylate reductase classified, for example, under EC 1.2.99.6, such as, for example, the gene product of car in combination with a polypeptide having the activity of a phosphopantetheine transferase enhancer (e.g., encoded by a sfp gene from Bacillus subtilis or npt gene from Nocardia) or the gene product of griC & griD from Streptomyces griseus (Suzuki et al, J. Antibiot., 2007, 60(6), 380-387); followed by conversion of 7-aminoheptanal to 7-aminoheptanol by a polypeptide having the activity of a ω-transaminase classified, for example, under EC 2.6.1.18, EC 2.6.1.19, EC 2.6.1.29, EC 2.6.1.48, or EC 2.6.1.82 such as, for example, SEQ ID NOs: 7-12, see above; followed by conversion to 7-aminoheptanal by a polypeptide having the activity of an alcohol dehydrogenase classified, for example, under EC 1.1.1.- (e.g., EC 1.1.1.1, EC 1.1.1.2, EC 1.1.1.21, or EC 1.1.1.184) such as, for example, the gene product of YMR318C from Saccharomyces cerevisiae or yqhD from Escherichia coli (Liu et al., Microbiology, 2009, 155, 2078-2085; Larroy et al, 2002, Biochem J., 361(Pt 1), 163-172; Jarboe, 2011, Appl. Microbial. Biotechnol., 89(2), 249-257) or a polypeptide represented by GenBank Accession No. CAA81612.1 (SEQ ID NO: 21); followed by conversion to heptamethylenediamine by a polypeptide having the activity of a ω-transaminase classified, for example, under EC 2.6.1.18, EC 2.6.1.19, EC 2.6.1.29, EC 2.6.1.48, or EC 2.6.1.82, such as, for example, SEQ ID NOs: 7-12, see above. See FIG. 5.

In some embodiments, heptamethylenediamine is synthesized from the central precursor, 7-aminoheptanoate (which can be produced as described in FIG. 4), by conversion of 7-aminoheptanoate to N7-acetyl-7-aminoheptanoate by a polypeptide having the activity of an N-acetyltransferase such as a lysine N-acetyltransferase classified, for example, under EC 2.3.1.32, such as, for example, the gene product of LYCI from Yarrowia lipolytica (UniProtKB Accession No. P41929), the gene product of ablB from Methanococcus maripaludis (UniProtKB Accession No. Q6LYX3), or the gene product of ablB from Methanosarcina mazei (UniProtKB Accession No. Q8PYC8); followed by conversion to N7-acetyl-7-aminoheptanal by a polypeptide having the activity of a carboxylate reductase classified, for example, under EC 1.2.99.6 such as, for example, the gene product of car (see above, e.g., SEQ ID NOs: 1-6) in combination with a polypeptide having the activity of a phosphopantetheine transferase enhancer (e.g., encoded by a sfp gene from Bacillus subtilis or npt gene from Nocardia) or the gene product of griC & griD from Streptomyces griseus (Suzuki et al., J. Antibiot., 2007, 60(6), 380-387; followed by conversion to N7-acetyl-1,7-diaminoheptane by a polypeptide having the activity of a ω-transaminase classified, for example, under EC 2.6.1.18, EC 2.6.1.19, EC 2.6.1.29, EC 2.6.1.48, or EC 2.6.1.82, such as SEQ ID NOs: 7-12, see above; followed by conversion to heptamethylenediamine by a polypeptide having the activity of a deacylase classified, for example, under EC 3.5.1.-, such as, for example, EC 3.5.1.62 or EC 3.5.1.82. See FIG. 6.

In some embodiments, heptamethylenediamine is synthesized from the central precursor, pimelate semialdehyde, by conversion of pimelate semialdehyde to heptanedial by a polypeptide having the activity of a carboxylate reductase classified, for example, under EC 1.2.99.6 such as, for example, the gene product of car (see above, e.g., SEQ ID NO: 5) in combination with a phosphopantetheine transferase enhancer (e.g., encoded by a sfp gene from Bacillus subtilis or npt gene from Nocardia) or the gene product of griC & griD from Streptomyces griseus (Suzuki et al., J. Antibiot., 2007, 60(6), 380-387) followed by conversion to 7-aminoheptanal by a polypeptide having the activity of a ω-transaminase classified, for example, under EC 2.6.1.18, EC 2.6.1.19, EC 2.6.1.29, EC 2.6.1.48, or EC 2.6.1.82; followed by conversion to heptamethylenediamine by a polypeptide having the activity of a ω-transaminase classified, for example, under EC 2.6.1.18, EC 2.6.1.19, EC 2.6.1.29, EC 2.6.1.48, or EC 2.6.1.82, such as, for example, SEQ ID NOs: 7-12. See FIG. 5.

Pathways Using 7-Hydroxyheptanoate as Central Precursor to 1,7-Heptanediol

In some embodiments, 1,7 heptanediol is synthesized from the central precursor, 7-hydroxyheptanoate (which can be produced as described in FIG. 6), by conversion of 7-hydroxyheptanoate to 7-hydroxyheptanal by a polypeptide having the activity of a carboxylate reductase classified, for example, under EC 1.2.99.6 such as, for example, the gene product of car (see above, e.g., SEQ ID NOs: 1-6) in combination with a polypeptide having the activity of a phosphopantetheine transferase enhancer (e.g., encoded by a sfp gene from Bacillus subtilis or npt gene from Nocardia) or the gene products of griC and griD from Streptomyces griseus (Suzuki et al, J. Antibiot., 2007, 60(6), 380-387); followed by conversion of 7-hydroxyheptanal to 1,7 heptanediol by a polypeptide having the activity of an alcohol dehydrogenase (classified, for example, under EC 1.1.1.- such as EC 1.1.1.1, EC 1.1.1.2, EC 1.1.1.21, or EC 1.1.1.184) such as, for example, the gene product of YMR318C from Saccharomyces cerevisiae or yqhD from Escherichia coli (see, e.g., Liu et al., Microbiology, 2009, 155, 2078-2085; Larroy et al., 2002, Biochem J., 361(Pt 1), 163-172; or Jarboe, 2011, Appl. Microbiol. Biotechnol., 89(2), 249-257), or a polypeptide represented by GenBank Accession No. CAA81612.1 (SEQ ID NO: 21) (from Geobacillus stearothermophilus). See FIG. 7.

Cultivation Strategy

In some embodiments, one or more C7 building blocks are biosynthesized in a recombinant microorganism using anaerobic, aerobic or micro-aerobic cultivation conditions. In some embodiments, the cultivation strategy entails nutrient limitation such as, for example, nitrogen, phosphate, or oxygen limitation.

In some embodiments, a cell retention strategy using, for example, ceramic hollow fiber membranes can be employed to achieve and maintain a high cell density during either fed-batch or continuous fermentation.

In some embodiments, the principal carbon source fed to the fermentation in the synthesis of one or more C7 building blocks can derive from biological or non-biological feedstocks.

In some embodiments, the biological feedstock can be or can derive from, monosaccharides, disaccharides, lignocellulose, hemicellulose, cellulose, lignin, levulinic acid and formic acid, triglycerides, glycerol, fatty acids, agricultural waste, condensed distillers' solubles, plant oils, or municipal waste.

The efficient catabolism of crude glycerol stemming from the production of biodiesel has been demonstrated in several microorganisms such as Escherichia coli, Cupriavidus necator, Pseudomonas oleavorans, Pseudomonas putida, and Yarrowia lipolytica (Lee et al., Appl. Bio. Biochem. Biotechnol., 2012, 166:1801-1813; Yang et al., Biotechnology for Biofuels, 2012, 5:13; Meijnen et al., Appl. Microbiol. Biotechnol., 2011, 90:885-893).

The efficient catabolism of lignocellulosic-derived levulinic acid has been 2 demonstrated in several organisms such as Cupriavidus necator and Pseudomonas putida in the synthesis of 3-hydroxyvalerate via the precursor propanoyl-CoA (Jaremko and Yu, 2011, supra; Martin and Prather, J. Biotechnol., 2009, 139:61-67).

The efficient catabolism of lignin-derived aromatic compounds such as benzoate analogues has been demonstrated in several microorganisms such as Pseudomonas putida, Cupriavidus necator (Bugg et al., Current Opinion in Biotechnology, 2011, 22, 394-400; Pérez-Pantoja et al., FEMS Microbiol. Rev., 2008, 32, 736-794).

The efficient utilization of agricultural waste, such as olive mill waste water has been demonstrated in several microorganisms, including Yarrowia lipolytica (Papanikolaou et al, Bioresour. Technol., 2008, 99(7):2419-2428).

The efficient utilization of fermentable sugars such as monosaccharides and disaccharides derived from cellulosic, hemicellulosic, cane and beet molasses, cassava, corn, and other agricultural sources has been demonstrated for several microorganism such as Escherichia coli, Corynebacterium glutamicum, Lactobacillus delbrueckii, and Lactococcus lactis (see, e.g., Hermann et al, J. Biotechnol., 2003, 104:155-172; Wee et al., Food Technol. Biotechnol, 2006, 44(2):163-172; Ohashi et al., J. Bioscience and Bioengineering, 1999, 87(5):647-654).

The efficient utilization of furfural, derived from a variety of agricultural lignocellulosic sources, has been demonstrated for Cupriavidus necator (Li et al., Biodegradation, 2011, 22:1215-1225).

In some embodiments, the non-biological feedstock can be or can derive from natural gas, syngas, CO₂/H₂, methanol, ethanol, benzoate, non-volatile residue (NVR) or a caustic wash waste stream from cycloheptane oxidation processes, or terephthalic acid/isophthalic acid mixture waste streams.

The efficient catabolism of methanol has been demonstrated for the methylotrophic yeast Pichia pastoris.

The efficient catabolism of ethanol has been demonstrated for Clostridium kluyveri (Seedorf et al., Proc. Natl. Acad. Sci. USA, 2008, 105(6) 2128-2133).

The efficient catabolism of CO₂ and H₂, which may be derived from natural gas and other chemical and petrochemical sources, has been demonstrated for Cupriavidus necator (Prybylski et al., Energy, Sustainability and Society, 2012, 2:11).

The efficient catabolism of syngas has been demonstrated for numerous microorganisms, such as Clostridium ljungdahlii and Clostridium autoethanogenum (Köpke et al., Applied and Environmental Microbiology, 2011, 77(15):5467-5475).

The efficient catabolism of the non-volatile residue waste stream from cycloheptane processes has been demonstrated for numerous microorganisms, such as Delftia acidovorans and Cupriavidus necator (Ramsay et al., Applied and Environmental Microbiology, 1986, 52(1): 152-156).

In some embodiments, the microorganism is a prokaryote. For example, the prokaryote can be a bacterium from the genus Escherichia such as Escherichia coli; from the genus Clostridia such as Clostridium ljungdahlii, Clostridium autoethanogenum, or Clostridium kluyveri; from the genus Corynebacteria such as Corynebacterium glutamicum; from the genus Cupriavidus such as Cupriavidus necator or Cupriavidus metallidurans; from the genus Pseudomonas such as Pseudomonas fluorescens, Pseudomonas putida, or Pseudomonas oleavorans; from the genus Delftia such as Delftia acidovorans; from the genus Bacillus such as Bacillus subtillis; from the genus Lactobacillus such as Lactobacillus delbrueckii; or from the genus Lactococcus such as Lactococcus lactis. Such prokaryotes also can be a source of genes to construct recombinant microorganisms described herein that are capable of producing one or more C7 building blocks.

In some embodiments, the microorganism is a eukaryote. For example, the eukaryote can be a filamentous fungus, e.g., one from the genus Aspergillus such as Aspergillus niger. Alternatively, the eukaryote can be a yeast, e.g., one from the genus Saccharomyces such as Saccharomyces cerevisiae; from the genus Pichia such as Pichia pastoris; or from the genus Yarrowia such as Yarrowia lipolytica; from the genus Issatchenkia such as Issathenkia orientalis; from the genus Debaryomyces such as Debaryomyces hansenii; from the genus Arxula such as Arxula adenoinivorans; or from the genus Kluyveromyces such as Kluyveromyces lactis. Such eukaryotes also can be a source of genes to construct recombinant microorganisms described herein that are capable of producing one or more C7 building blocks.

Metabolic Engineering

The present document provides methods involving less than all the steps described for all the above pathways. Such methods can involve, for example, one, two, three, four, five, six, seven, eight, nine, ten, eleven, twelve or more of such steps. Where less than all the steps are included in such a method, the first, and in some embodiments the only, step can be any one of the steps listed.

Furthermore, recombinant microorganisms described herein can include any combination of the above enzymes such that one or more of the steps, e.g., one, two, three, four, five, six, seven, eight, nine, ten, or more of such steps, can be performed within a recombinant microorganism. This document provides cells of any of the genera and species listed and genetically engineered to express one or more (e.g., one, two, three, four, five, six, seven, eight, nine, 10, 11, 12 or more) recombinant forms of any of the enzymes recited in the document. Thus, for example, the cells can contain exogenous nucleic acids encoding enzymes catalyzing one or more of the steps of any of the pathways described herein.

In addition, this document recognizes that where enzymes have been described as accepting CoA-activated substrates, analogous enzyme activities associated with [acp]-bound substrates exist that are not necessarily in the same enzyme class.

Also, this document recognizes that where enzymes have been described as accepting (R)-enantiomers of substrate, analogous enzyme activities associated with (S)-enantiomer substrates exist that are not necessarily in the same enzyme class.

This document also recognizes that where an enzyme is shown to accept a particular co-factor, such as NADPH, or co-substrate, such as acetyl-CoA, many enzymes are promiscuous in terms of accepting a number of different co-factors or co-substrates in catalyzing a particular enzyme activity. Also, this document recognizes that where enzymes have high specificity for e.g., a particular co-factor such as NADH, an enzyme with similar or identical activity that has high specificity for the co-factor NADPH may be in a different enzyme class.

In some embodiments, the enzymes in the pathways outlined herein are the result of enzyme engineering via non-direct or rational enzyme design approaches with aims of improving activity, improving specificity, reducing feedback inhibition, reducing repression, improving enzyme solubility, changing stereo-specificity, or changing co-factor specificity.

In some embodiments, the enzymes in the pathways outlined here can be gene dosed, i.e., overexpressed, into the resulting genetically modified organism via episomal or chromosomal integration approaches.

In some embodiments, genome-scale system biology techniques such as Flux Balance Analysis can be utilized to devise genome scale attenuation or knockout strategies for directing carbon flux to a C7 building block.

Attenuation strategies include, but are not limited to; the use of transposons, homologous recombination (double cross-over approach), mutagenesis, enzyme inhibitors and RNAi interference.

Attenuation strategies have been employed to increase the yield of desired end products of engineered metabolic pathways. For example, genetic manipulations previously studied to make succinate the major fermentation product in E. coli include deletion of the fermentative lactate dehydrogenase (LDH) pathway (Mat-Jan et al., 1989), deletion of both the LDH and pyruvate formate lyase (PFL) pathways (Bunch et al., 1997), and deletion of multiple pathways including PFL and LDH pathways with an additional ptsG mutation (Donnelly et al., 1998; Chatterjee et al., 2001). Overexpression of phosphoenolpyruvate carboxylase (PEPC) (Millard et al., 1996), overexpression of the malic enzyme (Stols and Donnelly, 1997; Hong and Lee, 2000), overexpression of pyruvate carboxylase (PYC) (Gokarn et al., 1998; Gokarn et al., 2000; Vemuri et al., 2002a), and overexpression of the heterologous Actinobacillus succinogenes phosphoenolpyruvate carboxykinase in a PEPC E. coli mutant (Kim et al., 2004) have also been studied to improve succinate yield from recombinant E. coli.

In some embodiments, fluxomic, metabolomic and transcriptomal data can be utilized to inform or support genome-scale system biology techniques, thereby devising genome scale attenuation or knockout strategies in directing carbon flux to a C7 building block.

In some embodiments, the microorganism's tolerance to high concentrations of a C7 building block can be improved through continuous cultivation in a selective environment.

In some embodiments, the microorganism's endogenous biochemical network can be attenuated or augmented to (1) ensure the intracellular availability of acetyl-CoA or malonyl-CoA, (2) create an NADH or NADPH imbalance that may only be balanced via the formation of one or more C7 building blocks, (3) prevent degradation of central metabolites, central precursors leading to and including one or more C7 building blocks, and/or (4) ensure efficient efflux from the cell.

In some embodiments requiring intracellular availability of acetyl-CoA for C7 building block synthesis, endogenous enzymes catalyzing the hydrolysis of acetyl-CoA such as short-chain length thioesterase can be attenuated in the microorganism.

In some embodiments requiring the intracellular availability of acetyl-CoA for C7 building block synthesis, an endogenous gene encoding a phosphotransacetylase generating acetate such as pta can be attenuated (Shen et al., Appl. Environ. Microbiol., 2011, 77(9):2905-2915).

In some embodiments requiring the intracellular availability of acetyl-CoA for C7 building block synthesis, an endogenous gene in an acetate synthesis pathway encoding an acetate kinase, such as ack, can be attenuated.

In some embodiments requiring the intracellular availability of acetyl-CoA and NADH for C7 building block synthesis, an endogenous gene encoding an enzyme that catalyzes the degradation of pyruvate to lactate such as lactate dehydrogenase encoded by IdhA can be attenuated (Shen et al., 2011, supra).

In some embodiments, enzymes that catalyze anapleurotic reactions such as PEP carboxylase and/or pyruvate carboxylase can be overexpressed in the microorganism.

In some embodiments requiring the intracellular availability of acetyl-CoA and NADH for C7 building block synthesis, endogenous genes encoding enzymes, such as menaquinol-fumarate oxidoreductase, that catalyze the degradation of phophoenolpyruvate to succinate such as frdBC can be attenuated (see, e.g., Shen et al., 2011, supra).

In some embodiments requiring the intracellular availability of acetyl-CoA and NADH for C7 building block synthesis, an endogenous gene encoding an enzyme that catalyzes the degradation of acetyl-CoA to ethanol such as, for example, the alcohol dehydrogenase encoded by adhE from Clostridium acetobutylicum can be attenuated (Shen et al., 2011, supra). In some embodiments, where pathways require excess NADH co-factor for C7 building block synthesis, a recombinant formate dehydrogenase gene, e.g., fdh1 from Candida boidinii, can be overexpressed in the microorganism (Shen et al., 2011, supra).

In some embodiments, where pathways require excess NADH co-factor for C7 building block synthesis, a recombinant NADH-consuming transhydrogenase can be attenuated.

In some embodiments, an endogenous gene encoding an enzyme that catalyzes go the degradation of pyruvate to ethanol such as pyruvate decarboxylase can be attenuated.

In some embodiments requiring the intracellular availability of acetyl-CoA for C7 building block synthesis, a recombinant acetyl-CoA synthetase such as, for example, the gene product of acsA from Cupriavidus necator can be overexpressed in the microorganism (Satoh et al., J. Bioscience and Bioengineering, 2003, 95(4):335-341).

In some embodiments, carbon flux can be directed into the pentose phosphate cycle to increase the supply of NADPH by attenuating an endogenous glucose-6-phosphate isomerase (EC 5.3.1.9).

In some embodiments, carbon flux can be redirected into the pentose phosphate cycle to increase the supply of NADPH by overexpression a 6-phosphogluconate dehydrogenase and/or a transketolase (Lee et al., 2003, Biotechnology Progress, 19(5), 1444-1449) from, for example, Escherichia coli.

In some embodiments, where pathways require excess NADPH co-factor in the synthesis of a C7 building block, a gene such as udhA from Escherichia coli encoding a puridine nucleotide transhydrogenase can be overexpressed in the microorganisms (Brigham et al., Advanced Biofuels and Bioproducts, 2012, Chapter 39, 1065-1090).

In some embodiments, where pathways require excess NADPH co-factor in the synthesis of a C7 Building Block, a recombinant glyceraldehyde-3-phosphate-dehydrogenase gene such as gapN from Sulfolobus solfataricus can be overexpressed in the microorganisms (Brigham et al., 2012, supra).

In some embodiments, where pathways require excess NADPH co-factor in the synthesis of a C7 building block, a recombinant malic enzyme gene such as maeA or maeB from Cupriavidus necator can be overexpressed in the microorganisms (Brigham et al., 2012, supra).

In some embodiments, where pathways require excess NADPH co-factor in the synthesis of a C7 building block, a recombinant glucose-6-phosphate dehydrogenase gene such as zwf from Escherichia coli can be overexpressed in the microorganisms (Lim et al., J. Bioscience and Bioengineering, 2002, 93(6), 543-549).

In some embodiments, where pathways require excess NADPH co-factor in the synthesis of a C7 building block, a recombinant fructose 1,6 diphosphatase gene such as fbp from Corynebacterium glutamicum can be overexpressed in the microorganisms (Becker et al, J. Biotechnol., 2007, 132:99-109).

In some embodiments, where pathways require excess NADPH co-factor in the synthesis of a C7 building block, endogenous triose phosphate isomerase (EC 5.3.1.1) can be attenuated.

In some embodiments, where pathways require excess NADPH co-factor in the synthesis of a C7 building block, a recombinant glucose dehydrogenase such as, for example, the gene product of gdh from Bacillus subtilis can be overexpressed in the microorganism (Satoh et al., J. Bioscience and Bioengineering, 2003, 95(4):335-341).

In some embodiments, endogenous enzymes facilitating the conversion of NADPH to NADH can be attenuated, such as, for example, the NADH generation cycle that may be generated via inter-conversion of glutamate dehydrogenases classified under EC 1.4.1.2 (NADH-specific) and EC 1.4.1.4 (NADPH-specific).

In some embodiments, an endogenous glutamate dehydrogenase (EC 1.4.1.3) that utilizes both NADH and NADPH as co-factors can be attenuated.

In some embodiments, a membrane-bound cytochrome P450 such as CYP4F3B can be solubilized by only expressing the cytosolic domain and not the N-terminal region that anchors the P450 to the endoplasmic reticulum (Scheller et al., J. Biol. Chem., 1994, 269(17):12779-12783).

In some embodiments, an enoyl-CoA reductase can be solubilized via expression as a fusion protein with a small soluble protein, for example, the maltose binding protein (Gloerich et al., FEBS Letters, 2006, 580, 2092-2096).

In some embodiments using microorganisms that naturally accumulate polyhydroxyalkanoates, the endogenous polymer synthase enzymes can be attenuated in the microorganism strain.

In some embodiments, a L-alanine dehydrogenase can be overexpressed in the microorganism to regenerate L-alanine from pyruvate as an amino donor for ω-transaminase catalyzed reactions. For example, the L-alanine dehydrogenase may be from Escherichia coli.

In some embodiments, an L-glutamate dehydrogenase, a L-glutamine synthetase, or an alpha-aminotransaminase can be overexpressed in the microorganism to regenerate L-glutamate from 2-oxoglutarate as an amino donor for ω-transaminase catalyzed reactions. For example, the L-glutamate dehydrogenase, the L-glutamine synthetase, or the alpha-aminotransaminase may be from Escherichia coli.

In some embodiments, enzymes such as a pimeloyl-CoA dehydrogenase classified, for example, under EC 1.3.1.62; an acyl-CoA dehydrogenase classified, for example, under EC 1.3.8.7, EC 1.3.8.1, or EC 1.3.99.-; and/or a butyryl-CoA dehydrogenase classified, for example, under EC 1.3.8.6 that degrade central metabolites and central precursors leading to and including C7 building blocks can be attenuated. Examples of polypeptides having the activity of an acyl-CoA dehydrogenase classified under EC 1.3.99.- include, but are not limited to, the gene product of atuD from Pseudomonas aeruginosa (UniProtKB Accession No. Q9HZV8), the gene product of scu from Drosophila melanogaster (UniProtKB Accession No. O18404), the gene product of fadE26 from Mycobacterium tuberculosis (UniProtKB Accession No. I6YCA3), the gene product of aidB from Escherichia coli (UniProtKB Accession No. P33224), the gene product of acdh-11 from Caenorhabditis elegans (UniProtKB Accession No. Q9XWZ2), and the gene product of Acad11 from Mus musculus (UniProtKB Accession No. Q80XL6).

In some embodiments, endogenous enzymes activating C7 building blocks via Coenzyme A esterification such as CoA-ligases (e.g., an adipyl-CoA synthetase) classified under, for example, EC 6.2.1.- can be attenuated.

In some embodiments, the efflux of a C7 building block across the cell membrane to the extracellular media can be enhanced or amplified by genetically engineering structural modifications to the cell membrane or increasing any associated transporter activity for a C7 building block.

The efflux of heptamethylenediamine can be enhanced or amplified by overexpressing broad substrate range multidrug transporters such as Bit from Bacillus subtilis (Woolridge et al., 1997, J. Biol. Chem., 272(14):8864-8866); AcrB and AcrD from Escherichia coli (Elkins & Nikaido, 2002, J. Bacteriol., 184(23), 6490-6499), NorA from Staphylococcus aereus (Ng et al, 1994, Antimicrob Agents Chemother, 38(6), 1345-1355), or Bmhr from Bacillus subtilis (Neyfakh, 1992, Antimicrob Agents Chemother, 36(2), 484-485).

The efflux of 7-aminoheptanoate and heptamethylenediamine can be enhanced or amplified by overexpressing the solute transporters such as, for example, the lysE transporter from Corynebacterium glutamicum (Bellmann et al., 2001, Microbiology, 147, 1765-1774).

The efflux of pimelic acid can be enhanced or amplified by overexpressing a dicarboxylate transporter such as, for example, the SucE transporter from Corynebacterium glutamicum (Huhn et al, Appl. Microbiol. & Biotech., 89(2), 327-335).

Metabolically engineering recombinant hosts with various enzymes to produce final products has been successfully demonstrated by several groups. See, e.g., Blombach B et al., Bioeng Bugs., 2011, 2(6):346-50 (teaching successful metabolic engineering of the last two steps of the Ehrlich pathway (by expression of genes encoding a broad range 2-ketoacid decarboxylase and an alcohol dehydrogenase) in recombinant hosts for the production of higher isobutanol); Adkins, J. et al, Front Microbiol., 2012, 3:313 (summarizing numerous biomonomers (such as polyester building-blocks) that can be produced as a result of metabolic and pathway engineering in various recombinant hosts); Chan, S. et al., Bioresour Technol., 2012, 103(1):329-36 (teaching production of succinic acid from sucrose and sugarcane molasses by metabolically engineering E. coli with sucrose-utilizing genes (cscKB and cscA)); Lee, S. et al., Appl Biochem Biotechnol., 2012, 167(1):24-38 (teaching successful metabolic engineering of P. aeruginosa and E. coli for improving long-chain fatty acid production by co-expressing essential enzymes that are involved in the fatty acid synthesis metabolic pathway (accA and fabD) as well as fatty acyl-acyl carrier protein thioesterase gene); Rathnasingh, C. et al., Biotechnol Bioeng., 2009, 104(4):729-39 (teaching successful metabolic engineering of E. coli for producing 3-hydroxypropionic acid from glycerol by overexpression of glycerol dehydratase (DhaB) and aldehyde dehydrogenase (AldH) along with glycerol dehydratase reactivase (GDR)).

Producing C7 Building Blocks Using a Recombinant Microorganism

Typically, one or more C7 building blocks can be produced by providing a microorganism and culturing the provided microorganism with a culture medium containing a suitable carbon source as described above. In general, the culture media and/or culture conditions can be such that the microorganisms grow to an adequate density and produce a C7 building block efficiently. For large-scale production processes, any method can be used such as those described elsewhere (Manual of Industrial Microbiology and Biotechnology, 2^(nd) Edition, Editors: A. L. Demain and J. E. Davies, ASM Press; and Principles of Fermentation Technology, P. F. Stanbury and A. Whitaker, Pergamon). Briefly, a large tank (e.g., a 100 gallon, 200 gallon, 500 gallon, or greater than 500 gallon tank) containing an appropriate culture medium is inoculated with a particular microorganism. After inoculation, the microorganism is incubated to allow biomass to be produced. Once a desired biomass is reached, the broth containing the microorganisms can be transferred to a second tank. This second tank can be any size. For example, the second tank can be larger, smaller, or the same size as the first tank. Typically, the second tank is larger than the first such that additional culture medium can be added to the broth from the first tank. In addition, the culture medium within this second tank can be the same as, or different from, that used in the first tank.

Once transferred, the microorganisms can be incubated to allow for the production of a C7 building block. Once produced, any method can be used to isolate C7 building blocks. For example, C7 building blocks can be recovered selectively from the fermentation broth via adsorption processes. In the case of pimelic acid and 7-aminoheptanoic acid, the resulting eluate can be further concentrated via evaporation, crystallized via evaporative and/or cooling crystallization, and the crystals recovered via centrifugation. In the case of heptamethylenediamine and 1,7-heptanediol, distillation may be employed to achieve the desired product purity.

The invention will be further described in the following examples, which do not limit the scope of the invention described in the claims.

EXAMPLES Example 1 Enzyme Activity of ω-Transaminase Using Pimelate Semialdehyde as Substrate and Forming 7-Aminoheptanoate

A nucleotide sequence encoding an N-terminal His-tag was added to the nucleic acid sequences from Chromobacterium violaceum, Pseudomonas syringae, Rhodobacter sphaeroides, and Vibrio fluvialis encoding the ω-transaminases of SEQ ID NOs: 7, 9, 10, and 12, respectively (see FIG. 8) such that N-terminal HIS tagged ω-transaminases could be produced. Each of the resulting modified genes was cloned into a pET21a expression so vector under control of the T7 promoter and each expression vector was transformed into a BL21[DE3] E. coli strain. The resulting recombinant E. coli strains were cultivated at 37° C. in a 250 mL shake flask culture containing 50 mL LB media and antibiotic selection pressure, with shaking at 230 rpm. Each culture was induced overnight at 16° C. using 1 mM IPTG.

The pellet from each induced shake flask culture was harvested via centrifugation. Each pellet was resuspended and lysed via sonication. The cell debris was separated from the supernatant via centrifugation and the cell free extract was used immediately in enzyme activity assays.

Enzyme activity assays in the reverse direction (i.e., 7-aminoheptanoate to pimelate semialdehyde) were performed in a buffer composed of a final concentration of 50 mM HEPES buffer (pH=7.5), 10 mM 7-aminoheptanoate, 10 mM pyruvate, and 100 μM pyridoxyl 5′ phosphate. Each enzyme activity assay reaction was initiated by adding cell free extract of the ω-transaminase gene product or the empty vector control to the assay buffer containing the 7-aminoheptanoate and incubated at 25° C. for 4 h, with shaking at 250 rpm. The formation of L-alanine from pyruvate was quantified via RP-HPLC.

Each enzyme only control without 7-aminoheptanoate demonstrated low base line conversion of pyruvate to L-alanine. See FIG. 14. The gene product of SEQ ID NO: 7, SEQ ID NO: 9, SEQ ID NO: 10, and SEQ ID NO: 12 accepted 7-aminoheptanoate as a substrate as confirmed against the empty vector control. See FIG. 15.

Enzyme activity in the forward direction (i.e., pimelate semialdehyde to 7-aminoheptanoate) was confirmed for the transaminases of SEQ ID NO: 9, SEQ ID NO: 10, and SEQ ID NO: 12. See FIG. 16. Enzyme activity assays were performed in a buffer composed of a final concentration of 50 mM HEPES buffer (pH=7.5), 10 mM pimelate semialdehyde, 10 mM L-alanine and 100 μM pyridoxyl 5′ phosphate. Each enzyme activity assay reaction was initiated by adding a cell free extract of the ω-transaminase gene product or the empty vector control to the assay buffer containing the pimelate semialdehyde and incubated at 25° C. for 4 h, with shaking at 250 rpm. The formation of pyruvate was quantified via RP-HPLC.

The gene products represented by SEQ ID NO: 9, SEQ ID NO: 10, and SEQ ID NO: 12 accepted pimelate semialdehyde as substrate as confirmed against the empty vector control. See FIG. 16. The reversibility of the ω-transaminase activity was confirmed, demonstrating that the ω-transaminases represented by SEQ ID NO: 7, SEQ ID NO: 9, SEQ ID NO: 10, and SEQ ID NO: 12 accepted 7-aminoheptanoate as substrate and synthesized pimelate semialdehyde as a reaction product. See FIG. 15.

Example 2 Enzyme Activity of Carboxylate Reductase Using Pimelate as Substrate and Forming Pimelate Semialdehyde

A nucleotide sequence encoding a HIS-tag was added to the nucleic acid sequences from Segniliparus rugosus and Segniliparus rotundus that encode the carboxylate reductases of SEQ ID NOs: 3 (EFV111917.1) and 6 (ADG98140.1), respectively (see FIG. 8), such that N-terminal HIS tagged carboxylate reductases could be produced. Each of the modified genes was cloned into a pET Duet expression vector along with a sfp gene encoding a HIS-tagged phosphopantetheine transferase from Bacillus subtilis, both under the T7 promoter. Each expression vector was transformed into a BL21[DE3] E. coli strain, and the resulting recombinant E. coli strains were cultivated at 37° C. in a 250 mL shake flask culture containing 50 mL LB media and antibiotic selection pressure, with shaking at 230 rpm. Each culture was induced overnight at 37° C. using an auto-induction media.

The pellet from each induced shake flask culture was harvested via centrifugation. Each pellet was resuspended and lysed via sonication, and the cell debris was separated from the supernatant via centrifugation. The carboxylate reductases and phosphopantetheine transferases were purified from the supernatant using Ni-affinity chromatography, diluted 10-fold into 50 mM HEPES buffer (pH=7.5), and concentrated via ultrafiltration.

Enzyme activity assays (i.e., from pimelate to pimelate semialdehyde) were performed in triplicate in a buffer composed of a final concentration of 50 mM HEPES buffer (pH=7.5), 2 mM pimelate, 10 mM MgCl₂, 1 mM ATP, and 1 mM NADPH. Each enzyme activity assay reaction was initiated by adding purified carboxylate reductase and phosphopantetheine transferase gene products or the empty vector control to the assay buffer containing the pimelate and then incubated at room temperature for 20 min. The consumption of NADPH was monitored by absorbance at 340 nm. Each enzyme only control without pimelate demonstrated low base line consumption of NADPH. See bars for EFV11917.1 and ADG98140.1 in FIG. 9.

The gene products represented by SEQ ID NO: 3 (EFV11917.1) and SEQ ID NO: 6 (ADG98140.1), enhanced by the gene product of sfp from Bacillus subtilis, accepted pimelate as a substrate, as confirmed against the empty vector control (see FIG. 10), and synthesized pimelate semialdehyde.

Example 3 Enzyme Activity of Carboxylate Reductase Using 7-Hydroxyheptanoate as Substrate and Forming 7-Hydroxyheptanal

A nucleotide sequence encoding a His-tag was added to the nucleic acids from Mycobacterium marinum, Mycobacterium smegmatis, Segniliparus rugosus, Mycobacterium massiliense, and Segniliparus rotundus that encode the carboxylate reductases of SEQ ID NOs: 1-6 respectively (see FIG. 8) such that N-terminal HIS tagged carboxylate reductases could be produced. Each of the modified genes was cloned into a pET Duet expression vector alongside a sfp gene encoding a His-tagged phosphopantetheine transferase from Bacillus subtilis, both under control of the T7 promoter. Each expression vector was transformed into a BL21[DE3] E. coli strain along with the expression vectors from Example 2. Each resulting recombinant E. coli strain was cultivated at 37° C. in a 250 mL shake flask culture containing 50 mL LB media and antibiotic selection pressure, with shaking at 230 rpm. Each culture was induced overnight at 37° C. using an auto-induction media.

The pellet from each induced shake flask culture was harvested via centrifugation. Each pellet was resuspended and lysed via sonication. The cell debris was separated from the supernatant via centrifugation. The carboxylate reductases and phosphopantetheine transferase were purified from the supernatant using Ni-affinity chromatography, diluted 10-fold into 50 mM HEPES buffer (pH=7.5) and concentrated via ultrafiltration.

Enzyme activity (i.e., 7-hydroxyheptanoate to 7-hydroxyheptanal) assays were performed in triplicate in a buffer composed of a final concentration of 50 mM HEPES buffer (pH=7.5), 2 mM 7-hydroxyheptanal, 10 mM MgCl₂, 1 mM ATP, and 1 mM NADPH. Each enzyme activity assay reaction was initiated by adding purified carboxylate reductase and phosphopantetheine transferase or the empty vector control to the assay buffer containing the 7-hydroxyheptanoate and then incubated at room temperature for 20 min. The consumption of NADPH was monitored by absorbance at 340 nm. Each enzyme only control without 7-hydroxyheptanoate demonstrated low base line consumption of NADPH. See FIG. 9.

The gene products represented by SEQ ID NO 1-6 enhanced by the gene product of sfp, accepted 7-hydroxyheptanoate as substrate as confirmed against the empty vector control (see FIG. 1), and synthesized 7-hydroxyheptanal.

Example 4 Enzyme Activity of ω-Transaminase for 7-Aminoheptanol, Forming 7-Oxoheptanol

A nucleotide sequence encoding an N-terminal His-tag was added to the Chromobacterium violaceum, Pseudomonas syringae, and Rhodobacter sphaeroides nucleic acids encoding the ω-transaminases of SEQ ID NOs: 7, 9, and 10, respectively (see FIG. 8) such that N-terminal HIS tagged ω-transaminases could be produced. The modified genes were cloned into a pET21a expression vector under the T7 promoter. Each expression vector was transformed into a BL21[DE3] E. coli strain. Each resulting recombinant E. coli strain were cultivated at 37° C. in a 250 mL shake flask culture containing 50 mL LB media and antibiotic selection pressure, with shaking at 230 rpm. Each culture was induced overnight at 16&C using 1 mM IPTG.

The pellet from each induced shake flask culture was harvested via centrifugation. Each pellet was resuspended and lysed via sonication. The cell debris was separated from the supernatant via centrifugation and the cell free extract was used immediately in enzyme activity assays.

Enzyme activity assays in the reverse direction (i.e., 7-aminoheptanol to 7-oxoheptanol) were performed in a buffer composed of a final concentration of 50 mM HEPES buffer (pH=7.5), 10 mM 7-aminoheptanol, 10 mM pyruvate, and 100 μM pyridoxyl 5′ phosphate. Each enzyme activity assay reaction was initiated by adding cell free extract of the ω-transaminase gene product or the empty vector control to the assay buffer containing the 7-aminoheptanol and then incubated at 25° C. for 4 h, with shaking at 250 rpm. The formation of L-alanine was quantified via RP-HPLC.

Each enzyme only control without 7-aminoheptanol had low base line conversion of pyruvate to L-alanine. See FIG. 14.

The gene products represented by SEQ ID NOs: 7, 9, and 10 accepted 7-aminoheptanol as substrate as confirmed against the empty vector control (see FIG. 19) and synthesized 7-oxoheptanol as reaction product. Given the reversibility of the ω-transaminase activity (see Example 1), it can be concluded that the gene products of SEQ ID NOs: 7, 9, and 10 accept 7-oxoheptanol as substrate and form 7-aminoheptanol.

Example 5 Enzyme Activity of ω-Transaminase Using Heptamethylenediamine as Substrate and Forming 7-Aminoheptanal

A nucleotide sequence encoding an N-terminal His-tag was added to the Chromobacterium violaceum, Pseudomonas aeruginosa, Pseudomonas syringae, Rhodobacter sphaeroides, Escherichia coli, and Vibrio fluvialis nucleic acids encoding the ω-transaminases of SEQ ID NOs: 7-12, respectively (see FIG. 8) such that N-terminal HIS tagged ω-transaminases could be produced. The modified genes were cloned into a pET21a expression vector under the T7 promoter. Each expression vector was transformed into a BL21 [DE3] E. coli strain. Each resulting recombinant E. coli strain were cultivated at 37° C. in a 250 mL shake flask culture containing 50 mL LB media and antibiotic selection pressure, with shaking at 230 rpm. Each culture was induced overnight at 16′C using 1 mM IPTG.

The pellet from each induced shake flask culture was harvested via centrifugation. Each pellet was resuspended and lysed via sonication. The cell debris was separated from the supernatant via centrifugation, and the cell free extract was used immediately in enzyme activity assays.

Enzyme activity assays in the reverse direction (i.e., heptamethylenediamine to 7 aminoheptanal) were performed in a buffer composed of a final concentration of 50 mM HEPES buffer (pH=7.5), 10 mM heptamethylenediamine, 10 mM pyruvate, and 100 μM pyridoxyl 5′ phosphate. Each enzyme activity assay reaction was initiated by adding cell free extract of the ω-transaminase gene product or the empty vector control to the assay buffer containing the heptamethylenediamine and then incubated at 25° C. for 4 h, with shaking at 250 rpm. The formation of L-alanine was quantified via RP-HPLC.

Each enzyme only control without heptamethylenediamine had low base line conversion of pyruvate to L-alanine. See FIG. 14.

The gene products of SEQ ID NOs: 7-12 accepted heptamethylenediamine as substrate as confirmed against the empty vector control (see FIG. 17) and synthesized 7-aminoheptanal as reaction product. Given the reversibility of the ω-transaminase activity (see Example 1), it can be concluded that the gene products of SEQ ID NOs: 7-12 accept 7-aminoheptanal as substrate and form heptamethylenediamine.

Example 6 Enzyme Activity of Carboxylate Reductase for N7-Acetyl-7-Aminoheptanoate, Forming N7-Acetyl-7-Aminoheptanal

The activity of each of the N-terminal His-tagged carboxylate reductases of SEQ ID NOs: 2, 5, and 6 (see Examples 2 and 3, and FIG. 8) for converting N7-acetyl-7-aminoheptanoate to N7-acetyl-7-aminoheptanal was assayed in triplicate in a buffer composed of a final concentration of 50 mM HEPES buffer (pH=7.5), 2 mM N7-acetyl-7-aminoheptanoate, 10 mM MgCl₂, 1 mM ATP, and 1 mM NADPH. The assays were initiated by adding purified carboxylate reductase and phosphopantetheine transferase or the empty vector control to the assay buffer containing the N7-acetyl-7-aminoheptanoate then incubated at room temperature for 20 min. The consumption of NADPH was monitored by absorbance at 340 nm. Each enzyme only control without N7-acetyl-7-aminoheptanoate demonstrated low base line consumption of NADPH. See FIG. 9.

The gene products of SEQ ID NOs: 2, 5, and 6, enhanced by the gene product of sfp, accepted N7-acetyl-7-aminoheptanoate as substrate as confirmed against the empty vector control (see FIG. 12), and synthesized N7-acetyl-7-aminoheptanal.

Example 7 Enzyme Activity of ω-Transaminase Using N7-Acetyl-1,7-Diaminoheptane, and Forming N7-Acetyl-7-Aminoheptanal

The activity of the N-terminal His-tagged ω-transaminases of SEQ ID NOs: 7-12 (see Example 5, and FIG. 8) for converting N7-acetyl-1,7-diaminoheptane to N7-acetyl-7-aminoheptanal was assayed using a buffer composed of a final concentration of 50 mM HEPES buffer (pH=7.5), 10 mM N7-acetyl-1,7-diaminoheptane, 10 mM pyruvate and 100 μM pyridoxyl 5′ phosphate. Each enzyme activity assay reaction was initiated by adding a cell free extract of the ω-transaminase or the empty vector control to the assay buffer containing the N7-acetyl-1,7-diaminoheptane then incubated at 25° C. for 4 h, with shaking at 250 rpm. The formation of L-alanine was quantified via RP-HPLC.

Each enzyme only control without N7-acetyl-1,7-diaminoheptane demonstrated low base line conversion of pyruvate to L-alanine. See FIG. 14.

The gene product of SEQ ID NOs: 7-12 accepted N7-acetyl-1,7-diaminoheptane as substrate as confirmed against the empty vector control (see FIG. 18) and synthesized N7-acetyl-7-aminoheptanal as reaction product.

Given the reversibility of the ω-transaminase activity (see Example 1), the gene products represented by SEQ ID NOs: 7-12 accept N7-acetyl-7-aminoheptanal as substrate forming N7-acetyl-1,7-diaminoheptane.

Example 8 Enzyme Activity of Carboxylate Reductase Using Pimelate Semialdehyde as Substrate and Forming Heptanedial

The N-terminal His-tagged carboxylate reductase of SEQ ID NO: 6 (see Example 3 and FIG. 8) was assayed using pimelate semialdehyde as substrate. The enzyme activity assay was performed in triplicate in a buffer composed of a final concentration of 50 mM HEPES buffer (pH=7.5), 2 mM pimelate semialdehyde, 10 mM MgCl₂, 1 mM ATP and 1 mM NADPH. The enzyme activity assay reaction was initiated by adding purified carboxylate reductase and phosphopantetheine transferase or the empty vector control to the assay buffer containing the pimelate semialdehyde and then incubated at room temperature for 20 min. The consumption of NADPH was monitored by absorbance at 340 nm. The enzyme only control without pimelate semialdehyde demonstrated low base line consumption of NADPH. See FIG. 9.

The gene product of SEQ ID NO: 6, enhanced by the gene product of sfp from Bacillus subtilis, accepted pimelate semialdehyde as substrate as confirmed against the empty vector control (see FIG. 13) and synthesized heptanedial.

OTHER EMBODIMENTS

It is to be understood that while the invention has been described in conjunction with the detailed description thereof, the foregoing description is intended to illustrate and not limit the scope of the invention, which is defined by the scope of the appended claims. Other aspects, advantages, and modifications are within the scope of the following claims. 

1. A method of producing non-3-enal and 9-oxononanoate in a recombinant microorganism, said method comprising enzymatically converting 9-hydroxyperoxyoctadec-10,12-dienoate to non-3-enal and 9-oxononanoate using an exogenous polypeptide having the activity of a hydroperoxide lyase classified under EC 4.2.99.-, said method optionally further comprising enzymatically converting non-3-enal to azelaic acid using one or more polypeptides comprising at least one polypeptide having the activity of a dodecenoyl-CoA isomerase classified under EC 5.3.3.8 or at least one polypeptide having the activity of an enoate reductase classified under EC 1.3.1.31.
 2. (canceled)
 3. (canceled)
 4. The method of claim 1, said method comprising enzymatically converting non-3-enal to azelaic acid using one or more polypeptides, comprising: at least one polypeptide having the activity of a dodecenoyl-CoA isomerase classified under EC 5.3.3.8, wherein said at least one polypeptide having the activity of a dodecenoyl-CoA isomerase classified under EC 5.3.3.8 enzymatically converts non-3-enoyl-CoA to non-2-enoyl-CoA; or at least one polypeptide having the activity of an enoate reductase classified under EC 1.3.1.31, wherein said at least one polypeptide having the activity of an enoate reductase classified under EC 1.3.1.31 enzymatically converts non-2-enal to nonanal, and optionally a polypeptide having the activity of a monooxygenase classified under EC 1.14.14.- or EC 1.14.15.-, wherein said polypeptide having the activity of a monooxygenase enzymatically converts nonanoic acid to 9-hydroxynonanoic acid. 5-8. (canceled)
 9. The method of claim 1, said method further comprising producing azelaic acid in the recombinant microorganism, wherein the method comprises the steps of enzymatically converting 9-hydroxyperoxyoctadec-10,12-dienoate to non-3-enal and 9-oxononanoate using an exogenous polypeptide having the activity of a hydroperoxide lyase classified under EC 4.2.99.- and enzymatically converting non-3-enal to azelaic acid using one or more polypeptides, including at least one polypeptide having the activity of a dodecenoyl-CoA isomerase classified under EC 5.3.3.8 or at least one polypeptide having the activity of an enoate reductase classified under EC 1.3.1.31.
 10. (canceled)
 11. The method of claim 9, wherein said non-3-enal is converted to azelaic acid using one or more polypeptides having the enzymatic activities of a monooxygenase, an enal isomerase, an aldehyde dehydrogenase, a CoA ligase, a dodecenoyl-CoA isomerase, a trans-2-enoyl-CoA reductase, a thioesterase, a monooxygenase, and/or an alcohol dehydrogenase. 12-17. (canceled)
 18. The method of claim 9, wherein said non-3-enal is converted to azelaic acid using one or more polypeptides having the enzymatic activities of a monooxygenase, an enoate reductase, an aldehyde dehydrogenase, a monooxygenase, and/or an alcohol dehydrogenase; or said 9-oxononanoate is converted to azelaic acid using a polypeptide having the enzymatic activity of an aldehyde dehydrogenase. 19-23. (canceled)
 24. The method of claim 9, said method further comprising enzymatically converting azelaic acid to pimeloyl-CoA using one or more polypeptides having the enzymatic activities of a CoA ligase, an acyl-CoA dehydrogenase, an enoyl-CoA hydratase, a 3-hydroxyacyl-CoA dehydrogenase, and/or a β-ketothiolase. 25-35. (canceled)
 36. The method of claim 24, said method further comprising enzymatically converting pimeloyl-CoA to one or more of pimelate semialdehyde, pimelic acid, 7-aminoheptanoate, 7-hydroxyheptanoate, heptamethylenediamine, or 1,7-heptanediol, or corresponding salts thereof, in one or more steps. 37-45. (canceled)
 46. The method of claim 36, wherein said pimeloyl-CoA is converted to pimelic acid using a polypeptide having the activity of a CoA ligase classified under EC 6.2.1.-., a polypeptide having the activity of a CoA transferase classified under EC 2.8.3.-, or a polypeptide having the activity of a thioesterase classified under EC 3.1.2.-. 47-49. (canceled)
 50. The method of claim 36, wherein said pimeloyl-CoA is converted to pimelate semialdehyde using one or more polypeptides having the activity of an acetylating aldehyde dehydrogenase; said method further comprising optionally converting pimelate semialdehyde to 7-aminoheptanoate using one or more polypeptides having the activity of a ω-transaminase classified under EC 2.6.1.-; converting pimelate semialdehyde to 7-hydroxyheptanoate using one or more polypeptides having the activity of an alcohol dehydrogenase, wherein said alcohol dehydrogenase is a 4-hydroxybutanoate dehydrogenase, a 5-hydroxypentanoate dehydrogenase, or a 6-hydroxyhexanoate dehydrogenase; or converting pimelate semialdehyde to heptanedial using one or more polypeptides having the activity of a carboxylase reductase classified under EC 1.2.99.6; converting heptanedial to 7-aminoheptanal using one or more polypeptides having the activity of a ω-transaminase classified under EC 2.6.1.18, EC 2.6.1.19, EC 2.6.1.48, EC 2.6.1.29, or EC 2.6.1.82; and converting 7-aminoheptanal to heptamethylenediamine using one or more polypeptides having the activity of a ω-transaminase classified under EC 2.6.1.-. 51-54. (canceled)
 55. The method of claim 50, wherein pimelate semialdehyde is converted to 7-aminoheptanoate, said method further comprising converting said 7-aminoheptanoate to 7-aminoheptanal using one or more polypeptides having the activity of a carboxylase reductase classified under EC 1.2.99.6, and converting said 7-aminoheptanal to heptamethylenediamine using one or more polypeptides having the activity of a ω-transaminase classified under EC 2.6.1.-; or converting 7-aminoheptanoate to N7-acetyl-7-aminoheptanoate using one or more polypeptides having the activity of an N-acetyltransferase classified under EC 2.3.1.32; converting N7-acetyl-7-aminoheptanoate to N7-acetyl-7-aminoheptanal using one or more polypeptides having the activity of a carboxylase reductase classified under EC 1.2.99.6; converting N7-acetyl-7-aminoheptanal is converted to N7-acetyl-1,7-diaminoheptane using one or more polypeptides having the activity of a ω-transaminase classified under EC 2.6.1.-; and converting N7-acetyl-1,7-diaminoheptane to heptamethylenediamine using one or more polypeptides having the activity of a deacylase classified under EC 3.5.1.-. 56-59. (canceled)
 60. The method of claim 50, wherein pimelate semialdehyde is converted to 7-hydroxyheptanoate, said method further comprising converting said 7-hydroxyheptanoate to 7-hydroxyheptanal using one or more polypeptides having the activity of a carboxylase reductase classified under EC 1.2.99.6; converting 7-hydroxyheptanal to 7-aminoheptanol using one or more polypeptides having the activity of a ω-transaminase classified under EC 2.6.1.18, EC 2.6.1.19, or EC 2.6.1.48; converting 7-aminoheptanol to 7-aminoheptanal using one or more polypeptides having the activity of an alcohol dehydrogenase classified under EC 1.1.1.-; and converting 7-aminoheptanal to heptamethylenediamine using one or more polypeptides having the activity of a ω-transaminase classified under EC 2.6.1.-; or converting 7-hydroxyheptanoate to 7-hydroxyheptanal using a carboxylase reductase classified under EC 1.2.99.6; and converting 7-hydroxyheptanal to 1,7 heptanediol using one more polypeptides having the activity of an alcohol dehydrogenase classified under EC 1.1.1.-. 61-65. (canceled)
 66. The method of claim 65, wherein said 9-hydroxyperoxyoctadec-10,12-dienoate is enzymatically produced from octadecanoyl-CoA using one or more polypeptides having the activity of a delta9-desaturase, a delta12-desaturase, a thioesterase, and/or a 9-lipoxygenase. 67-70. (canceled)
 71. The method of claim 1, wherein said method is performed in a recombinant microorganism.
 72. The method of claim 71, wherein said microorganism is subjected to a cultivation strategy under aerobic, anaerobic, or micro-aerobic cultivation conditions and/or said microorganism is cultured under conditions of nutrient limitation.
 73. (canceled)
 74. (canceled)
 75. The method of claim 71, wherein the principal carbon source fed to the fermentation derives from a biological feedstock.
 76. The method of claim 75, wherein the biological feedstock is, or derives from, monosaccharides, disaccharides, lignocellulose, hemicellulose, cellulose, lignin, levulinic acid, formic acid, triglycerides, glycerol, fatty acids, agricultural waste, condensed distillers' solubles, plant oils, or municipal waste.
 77. The method of claim 71, wherein the principal carbon source fed to the fermentation derives from a non-biological feedstock.
 78. The method of claim 77, wherein the non-biological feedstock is, or derives from, natural gas, syngas, CO₂/H₂, methanol, ethanol, benzoate, non-volatile residue (NVR) caustic wash waste stream from cycloheptane oxidation processes, or terephthalic acid/isophthalic acid mixture waste streams.
 79. The method of claim 71, wherein the microorganism is a prokaryote.
 80. The method of claim 79, wherein said prokaryote is from a genus selected from Escherichia, Clostridia, Corynebacteria, Cupriavidus, Pseudomonas, Delftia, Bacillus, Lactobacillus, Lactococcus, and Rhodococcus.
 81. (canceled)
 82. The method of claim 71, wherein the microorganism is a eukaryote.
 83. The method of claim 82, wherein said eukaryote is from a genus selected from Aspergillus, Saccharomyces, Pichia, Yarrowia, Issatchenkia, Debaryomyces, Arxula, and Kluyveromyces. 84-86. (canceled)
 87. The method of claim 71, wherein said microorganism comprises an attenuation to one or more of the following enzymes: a polyhydroxyalkanoate synthase, an acetyl-CoA thioesterase, a phosphotransacetylase forming acetate, an acetate kinase, a lactate dehydrogenase, a menaquinol-fumarate oxidoreductase, an alcohol dehydrogenase forming ethanol, a triose phosphate isomerase, a pyruvate decarboxylase, a glucose-6-phosphate isomerase, an NADH-consuming transhydrogenase, an NADH-specific glutamate dehydrogenase, an NADH/NADPH-utilizing glutamate dehydrogenase, a pimeloyl-CoA dehydrogenase; an acyl-CoA dehydrogenase accepting C7 building blocks and central precursors as substrates; a butaryl-CoA dehydrogenase; or an adipyl-CoA synthetase.
 88. The method of claim 71, wherein said microorganism overexpresses one or more genes encoding: an acetyl-CoA synthetase, a 6-phosphogluconate dehydrogenase; a transketolase; a puridine nucleotide transhydrogenase; a glyceraldehyde-3P-dehydrogenase; a malic enzyme; a glucose-6-phosphate dehydrogenase; a glucose dehydrogenase; a fructose 1,6 diphosphatase; a L-alanine dehydrogenase; a L-glutamate dehydrogenase; a formate dehydrogenase; a L-glutamine synthetase; a diamine transporter, a dicarboxylate transporter, and/or a multidrug transporter.
 89. A recombinant microorganism producing azelaic acid, said microorganism comprising one or more nucleic acids encoding a polypeptide having the enzymatic activities of any one or more of the following enzymes: (i) a hydroperoxide lyase, (ii) an aldehyde dehydrogenase, (iii) a CoA ligase, (iv) a dodecenoyl-CoA isomerase, (v) a trans-2-enoyl-CoA reductase, (vi) a thioesterase, (vii) a monooxygenase, and/or (viii) an alcohol dehydrogenase; (ix) a hydroperoxide lyase, (x) an enoate reductase, (xi) an aldehyde dehydrogenase, (xii) a monooxygenase, and/or (xiii) an alcohol dehydrogenase; or (xiv) a hydroperoxide lyase, and/or (xv) an aldehyde dehydrogenase, wherein at least one of the nucleic acids is exogenous.
 90. (canceled)
 91. (canceled)
 92. The recombinant microorganism of claim 89, said microorganism further comprising one or more exogenous nucleic acids encoding a polypeptide having one or more of the enzymatic activities of: (i) a CoA ligase, (ii) an acyl-CoA dehydrogenase, (iii) an enoyl-CoA hydratase, (iv) a 3-hydroxyacyl-CoA dehydrogenase or a 3-oxoacyl ACP reductase, and/or (v) a β-ketothiolase, said microorganism further producing pimeloyl-CoA.
 93. The recombinant microorganism of claim 92, said microorganism further comprising one or more exogenous nucleic acids encoding a polypeptide having one or more of the enzymatic activities of a thioesterase, a CoA ligase, a CoA transferase, an acetylating aldehyde dehydrogenase, an alcohol dehydrogenase, an N-acetyltransferase, a deacylase, a ω-transaminase, a carboxylate reductase, and/or an aldehyde dehydrogenase, said microorganism further producing one or more of pimelic acid, 7-aminoheptanoate, 7-hydroxyheptanoate, heptamethylenediamine, and 1,7-heptanediol. 94-100. (canceled)
 101. The recombinant microorganism of claim 89, said microorganism further comprising one or more nucleic acids encoding a polypeptide having one or more of the enzymatic activities of a delta9-desaturase, a delta12-desaturase, a thioesterase, or a 9-lipoxygenase.
 102. (canceled)
 103. A nucleic acid construct or expression vector comprising a polynucleotide encoding a polypeptide having carboxylate reductase activity or a polynucleotide encoding a polypeptide having ω-transaminase activity, wherein the polynucleotide encoding a polypeptide having carboxylate reductase activity is operably linked to one or more heterologous control sequences that direct production of the polypeptide and wherein the polypeptide having carboxylate reductase activity is selected from: (a) a polypeptide having at least 70% sequence identity to the polypeptide of SEQ ID NO: 1; (b) a polypeptide having at least 70% sequence identity to the polypeptide of SEQ ID NO: 2; (c) a polypeptide having at least 70% sequence identity to the polypeptide of SEQ ID NO: 3; (d) a polypeptide having at least 70% sequence identity to the polypeptide of SEQ ID NO: 4, (e) a polypeptide having at least 70% sequence identity to the polypeptide of SEQ ID NO: 5 and (f) a polypeptide having at least 70% sequence identity to the polypeptide of SEQ ID NO: 6; and the polynucleotide encoding a polypeptide having ω-transaminase activity is operably linked to one or more heterologous control sequences that direct production of the polypeptide and wherein the polypeptide having ω-transaminase activity is selected from: (g) a polypeptide having at least 70% sequence identity to the polypeptide of SEQ ID NO: 7; (h) a polypeptide having at least 70% sequence identity to the polypeptide of SEQ ID NO: 8; (i) a polypeptide having at least 70% sequence identity to the polypeptide of SEQ ID NO: 9; (i) a polypeptide having at least 70% sequence identity to the polypeptide of SEQ ID NO: 10; (k) a polypeptide having at least 70% sequence identity to the polypeptide of SEQ ID NO: 11 or SEQ ID NO: 48; and (l) a polypeptide having at least 70% sequence identity to the polypeptide of SEQ ID NO:
 12. 104. (canceled)
 105. A composition comprising the nucleic acid construct or expression vector of claim
 103. 106. A culture medium comprising the nucleic acid construct or expression vector of claim
 103. 107-110. (canceled)
 111. Means for producing pimeloyl-CoA, comprising culturing a non-naturally occurring microorganism comprising at least one exogenous nucleic acid encoding a polypeptide having the enzymatic activity of (i) a hydroperoxide lyase, (ii) an aldehyde dehydrogenase, (iii) a CoA ligase, (iv) a dodecenoyl-CoA isomerase, (iv) a trans-2-enoyl-CoA reductase, (v) a thioesterase, (vi) an enoate reductase, (vii) a monooxygenase, (viii) an alcohol dehydrogenase, (ix) an acyl-CoA dehydrogenase, (x) an enoyl-CoA hydratase, (xi) a 3-hydroxyacyl-CoA dehydrogenase and (xii) a β-ketothiolase, expressed in a sufficient amount in said microorganism to produce pimeloyl-CoA.
 112. A bio-derived, bio-based, or fermentation-derived product, wherein said product comprises: (i) a composition comprising at least one bio-derived, bio-based, or fermentation-derived compound produced by a method according to claim 1 or any combination thereof, (ii) a bio-derived, bio-based, or fermentation-derived polymer comprising the bio-derived, bio-based or fermentation-derived composition or compound of (i), or any combination thereof, (iii) a bio-derived, bio-based, or fermentation-derived resin comprising the bio-derived, bio-based, or fermentation-derived compound or bio-derived, bio-based, or fermentation-derived composition of (i) or any combination thereof or the bio-derived, bio-based, or fermentation-derived polymer of (ii) or any combination thereof, (iv) a molded substance obtained by molding the bio-derived, bio-based, or fermentation-derived polymer of (ii) or the bio-derived, bio-based, or fermentation-derived resin of (iii), or any combination thereof, (v) a bio-derived, bio-based, or fermentation-derived formulation comprising the bio-derived, bio-based, or fermentation-derived composition of (i), bio-derived, bio-based, or fermentation-derived compound of (i), bio-derived, bio-based, or fermentation-derived polymer of (ii), bio-derived, bio-based, or fermentation-derived resin of (iii), or bio-derived, bio-based, or fermentation-derived molded substance of (v), or any combination thereof, or (vi) a bio-derived, bio-based, or fermentation-derived semi-solid or a non-semi-solid stream, comprising the bio-derived, bio-based, or fermentation-derived composition of (i), bio-derived, bio-based, or fermentation-derived compound of (i), bio-derived, bio-based, or fermentation-derived polymer of (ii), bio-derived, bio-based, or fermentation-derived resin of (iii), bio-derived, bio-based, or fermentation-derived formulation of (v), or bio-derived, bio-based, or fermentation-derived molded substance of (iv), or any combination thereof. 